reformatting

richard-burhans · Apr 16, 2024 · 44b09d6 · 44b09d6
1 parent 8a84931
commit 44b09d6
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Showing 8 changed files with 71 additions and 50 deletions.
diff --git a/tools/segalign/output_options.xml b/tools/segalign/output_options.xml
@@ -1,8 +1,8 @@
 <macros>
     <xml name="output_options">
         <section name="output_options" expanded="false" title="Output Options">
-            <yield />
-            <param argument="--markend" type="boolean" value="false" label="Write a marker line just before completion" />
+            <yield/>
+            <param argument="--markend" type="boolean" value="false" label="Write a marker line just before completion"/>
         </section>
     </xml>
 </macros>
diff --git a/tools/segalign/scoring_options.xml b/tools/segalign/scoring_options.xml
@@ -1,11 +1,25 @@
 <macros>
     <xml name="scoring_options">
         <section name="scoring_options" expanded="false" title="Scoring Options">
-            <param argument="--scoring" type="data" value="false" optional="true" format="txt" label="Scoring file in LASTZ format" />
-            <!--
-              ambiguous can be: {"n", "n,int,int", "iupac", "iupac,int,int"}
-              ints are ambiguous_reward and ambiguous_penalty
-            -->
+            <param argument="--scoring" type="data" value="false" optional="true" format="txt" label="Scoring file in LASTZ format"/>
+            <param name="ambiguous_selector" type="select" label="Ambiguous Nucleotides">
+                <option value="x" selected="true">None</option>
+                <option value="n">N</option>
+                <option value="iupac">IUPAC</option>
+            </param>
+            <conditional name="ambiguous_params">
+                <param name="set_ambiguous_params_selector" type="select" label="Set Ambiguous Nucleotide Scoring Parameters">
+                    <option value="false" selected="true">No</option>
+                    <option value="true">Yes</option>
+                </param>
+                <when value="false">
+                    <!-- Do nothing -->
+                </when>
+                <when value="true">
+                    <param name="ambiguous_reward" type="integer" value="0" label="Ambiguous Nucleotide Reward"/>
+                    <param name="ambiguous_penalty" type="integer" value="0" label="Ambiguous Nucleotide Penalty"/>
+                </when>
+            </conditional>
         </section>
     </xml>
 </macros>
diff --git a/tools/segalign/seeding_options.xml b/tools/segalign/seeding_options.xml
@@ -14,9 +14,9 @@
                     <!-- Do nothing -->
                 </when>
                 <when value="custom">
-                     <param name="custom_seed" type="text" value="" optional="false" label="Custom seed pattern">
-                         <validator type="empty_field"/>
-                         <!--
+                    <param name="custom_seed" type="text" value="" optional="false" label="Custom seed pattern">
+                        <validator type="empty_field"/>
+                        <!--
                          <validator type="regex" message="Arbitrary pattern of 1s, 0s, and Ts">^[01T]+$</validator>
                          <sanitizer invalid_char="">
                              <valid initial="none">
@@ -26,11 +26,11 @@
                              </valid>
                          </sanitizer>
                          -->
-                     </param>
+                    </param>
                 </when>
             </conditional>
-            <param argument="--step" type="integer" value="1" label="Offset between the starting positions of successive target words considered for generating seed table" />
-            <param argument="--notransition" type="boolean" checked="false" label="Don't allow one transition in a seed hit" />
+            <param argument="--step" type="integer" value="1" label="Offset between the starting positions of successive target words considered for generating seed table"/>
+            <param argument="--notransition" type="boolean" checked="false" label="Don't allow one transition in a seed hit"/>
         </section>
     </xml>
 </macros>
diff --git a/tools/segalign/segalign.xml b/tools/segalign/segalign.xml
@@ -67,29 +67,29 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
             --seed '$mode.seeding_options.seed.seed_selector'
 #end if
             --step '$mode.seeding_options.step'
-#if str($mode.seeding_options.notransition) == 'true'
+#if str($mode.seeding_options.notransition) == "true"
             --notransition
 #end if
 
 ## Ungapped Extension Options ------------------------------------------
 
             --xdrop '$mode.ungapped_extension_options.xdrop'
             --hspthresh '$mode.ungapped_extension_options.hspthresh'
-#if str($mode.ungapped_extension_options.noentropy) == 'true'
+#if str($mode.ungapped_extension_options.noentropy) == "true"
             --noentropy
 #end if
 
 ## Gapped Extension Options --------------------------------------------
 
 #if $segalign_mode != "segalign_repeat_masker"
-    #if str($mode.gapped_extension_options.nogapped) == 'true'
+    #if str($mode.gapped_extension_options.nogapped) == "true"
             --nogapped
     #end if
             --ydrop '$mode.gapped_extension_options.ydrop'
     #if str($mode.gapped_extension_options.gappedthresh) != ""
             --gappedthresh '$mode.gapped_extension_options.gappedthresh'
     #end if
-    #if str($mode.gapped_extension_options.notrivial) == 'true'
+    #if str($mode.gapped_extension_options.notrivial) == "true"
             --notrivial
     #end if
 #end if
@@ -129,7 +129,7 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
             --M '$mode.output_options.M'
             --output '$segalign_repeat_masker_output'
 #end if
-#if str($mode.output_options.markend) == 'true'
+#if str($mode.output_options.markend) == "true"
             --markend
 #end if
 
@@ -139,7 +139,7 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
             --lastz_interval_size '$mode.system_options.lastz_interval_size'
             --seq_block_size '$mode.system_options.seq_block_size'
             --num_gpu '$mode.system_options.num_gpu'
-#if str($mode.system_options.debug) == 'true'
+#if str($mode.system_options.debug) == "true"
             --debug
 #end if
 
@@ -158,43 +158,43 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
                 <option value="segalign_repeat_masker">SegAlign repeat masker</option>
             </param>
             <when value="segalign">
-                <param name="target" type="data" format="fasta" label="Target sequence file in FASTA format" />
-                <param name="query" type="data" format="fasta" label="Query sequence file in FASTA format" />
-                <expand macro="sequence_options" />
+                <param name="target" type="data" format="fasta" label="Target sequence file in FASTA format"/>
+                <param name="query" type="data" format="fasta" label="Query sequence file in FASTA format"/>
+                <expand macro="sequence_options"/>
                 <expand macro="scoring_options"/>
-                <expand macro="seeding_options" />
+                <expand macro="seeding_options"/>
                 <expand macro="ungapped_extension_options"/>
                 <expand macro="gapped_extension_options"/>
                 <expand macro="output_options">
                     <expand macro="segalign_output_options"/>
                 </expand>
-                <expand macro="system_options" />
+                <expand macro="system_options"/>
                 <section name="diagonal_partition_options" title="Diagonal Partition Options">
-                    <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization" />
-                    <param argument="--max_segments" type="integer" value="20000" label="Max segments" />
+                    <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/>
+                    <param argument="--max_segments" type="integer" value="20000" label="Max segments"/>
                 </section>
             </when>
             <when value="segalign_repeat_masker">
-                <param name="seq_file" type="data" format="fasta" label="Sequence file in FASTA format" />
+                <param name="seq_file" type="data" format="fasta" label="Sequence file in FASTA format"/>
                 <expand macro="sequence_options">
-                    <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to" />
+                    <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to"/>
                 </expand>
                 <expand macro="scoring_options"/>
-                <expand macro="seeding_options" />
+                <expand macro="seeding_options"/>
                 <expand macro="ungapped_extension_options"/>
                 <expand macro="output_options">
-                    <param argument="--M" type="integer" value="1" max="255" label="report any position that is covered by at least this many alignments; the maximum allowed depth is 255" />
+                    <param argument="--M" type="integer" value="1" max="255" label="report any position that is covered by at least this many alignments; the maximum allowed depth is 255"/>
                 </expand>
-                <expand macro="system_options" />
+                <expand macro="system_options"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
         <data name="segalign_output" format="tabular" label="SegAlign on ${on_string}">
             <change_format>
-                <when input="mode.output_options.format.format_selector" value="bam" format="bam" />
-                <when input="mode.output_options.format.format_selector" value="maf" format="maf" />
-                <when input="mode.output_options.format.format_selector" value="differences" format="interval" />
+                <when input="mode.output_options.format.format_selector" value="bam" format="bam"/>
+                <when input="mode.output_options.format.format_selector" value="maf" format="maf"/>
+                <when input="mode.output_options.format.format_selector" value="differences" format="interval"/>
             </change_format>
             <filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is False</filter>
         </data>
@@ -206,10 +206,16 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
         </data>
     </outputs>
     <tests>
-        <test>
-            <param name="target" value="hg38.chr20.chunk.fa.gz" type="fasta" />
-            <param name="query" value="mm39.chr2.chunk.fa.gz" type="fasta" />
-            <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf" />
+        <test expect_num_outputs="1">
+            <param name="mode_selector" value="segalign"/>
+            <param name="mode_selector" value="segalign_repeat_masker"/>
+            <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta"/>
+            <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="mode_selector" value="segalign_repeat_masker"/>
+            <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/>
+            <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="maf"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/segalign/segalign_output_options.xml b/tools/segalign/segalign_output_options.xml
@@ -68,8 +68,10 @@
                     <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
                     <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
                     <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
-                    <sanitizer invalid_char=""> 
-                        <valid initial="string.letters,string.digits"><add value="%" /> </valid>
+                    <sanitizer invalid_char="">
+                        <valid initial="string.letters,string.digits">
+                            <add value="%"/>
+                        </valid>
                     </sanitizer>
                 </param>
             </when>
@@ -89,4 +91,3 @@
         </conditional>
     </xml>
 </macros>
-
diff --git a/tools/segalign/sequence_options.xml b/tools/segalign/sequence_options.xml
@@ -6,7 +6,7 @@
                 <option value="minus">minus</option>
                 <option value="both" selected="true">both</option>
             </param>
-            <yield />
+            <yield/>
         </section>
     </xml>
 </macros>
diff --git a/tools/segalign/system_options.xml b/tools/segalign/system_options.xml
@@ -1,11 +1,11 @@
 <macros>
     <xml name="system_options">
         <section name="system_options" title="System Options">
-            <param argument="--wga_chunk_size" type="integer" value="250000" label="Chunk sizes for GPU calls for Xdrop - ⚠ change only if you are a developer" />
-            <param argument="--lastz_interval_size" type="integer" value="10000000" label="LASTZ interval for Ydrop - ⚠ change only if you are a developer" />
-            <param argument="--seq_block_size" type="integer" value="500000000" label="LASTZ interval for Ydrop - ⚠ change only if you are a developer" />
-            <param argument="--num_gpu" type="integer" value="-1" label="Specify number of GPUs to use - -1 if all the GPUs should be used" />
-            <param argument="--debug" type="boolean" value="false" label="Print debug messages" />
+            <param argument="--wga_chunk_size" type="integer" value="250000" label="Chunk sizes for GPU calls for Xdrop - ⚠ change only if you are a developer"/>
+            <param argument="--lastz_interval_size" type="integer" value="10000000" label="LASTZ interval for Ydrop - ⚠ change only if you are a developer"/>
+            <param argument="--seq_block_size" type="integer" value="500000000" label="LASTZ interval for Ydrop - ⚠ change only if you are a developer"/>
+            <param argument="--num_gpu" type="integer" value="-1" label="Specify number of GPUs to use - -1 if all the GPUs should be used"/>
+            <param argument="--debug" type="boolean" value="false" label="Print debug messages"/>
         </section>
     </xml>
 </macros>
diff --git a/tools/segalign/ungapped_extension_options.xml b/tools/segalign/ungapped_extension_options.xml
@@ -1,9 +1,9 @@
 <macros>
     <xml name="ungapped_extension_options">
         <section name="ungapped_extension_options" expanded="false" title="Ungapped Extension Options">
-            <param argument="--xdrop" type="integer" value="910" label="X-drop value for gap-free extension" />
-            <param argument="--hspthresh" type="integer" value="3000" label="Segment score threshold for high scoring pairs" />
-            <param argument="--noentropy" type="boolean" checked="false" label="Don't adjust low score segment pair scores using entropy factor after filtering stage" />
+            <param argument="--xdrop" type="integer" value="910" label="X-drop value for gap-free extension"/>
+            <param argument="--hspthresh" type="integer" value="3000" label="Segment score threshold for high scoring pairs"/>
+            <param argument="--noentropy" type="boolean" checked="false" label="Don't adjust low score segment pair scores using entropy factor after filtering stage"/>
         </section>
     </xml>
 </macros>