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Maker: add an option to warn users about license (#4390)
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* Maker: add an option to warn users about license (as asked by authors in galaxyproject/iwc#47 (comment))

* lint

* simpler check
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@abretaud
abretaud authored Feb 8, 2022
1 parent 42a0483 commit 739da8b
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Showing 2 changed files with 38 additions and 31 deletions.
2 changes: 1 addition & 1 deletion tools/maker/macros.xml
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Expand Up @@ -7,7 +7,7 @@
</requirements>
</xml>
<token name="@VERSION@">2.31.11</token>
<token name="@SUFFIX_VERSION@">1</token>
<token name="@SUFFIX_VERSION@">2</token>

<xml name="citations">
<citations>
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67 changes: 37 additions & 30 deletions tools/maker/maker.xml
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@@ -1,12 +1,12 @@
<?xml version="1.0"?>
<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_VERSION@">
<description>genome annotation pipeline</description>
<xrefs>
<xref type="bio.tools">maker</xref>
</xrefs>
<macros>
<import>macros.xml</import>
</macros>
<xrefs>
<xref type="bio.tools">maker</xref>
</xrefs>
<expand macro="requirements"/>
<command><![CDATA[
RM_PATH=\$(which RepeatMasker) &&
Expand Down Expand Up @@ -245,6 +245,12 @@ TMP= # specify a directory other than the system default temporary directory for
</configfiles>

<inputs>
<!-- More info on licensing in https://github.com/galaxyproject/iwc/pull/47#issuecomment-962260646 -->
<param name="license_agreement" type="boolean" label="Are you running Maker for academic use, or did you purchase a license?"
help="The MAKER authors specifically allowed to make it available on Galaxy. MAKER is free for academic use, but commercial Galaxy users of MAKER still need a license, which can be obtained at http://weatherby.genetics.utah.edu/cgi-bin/registration/maker_license.cgi">
<validator type="expression" message="You must either run Maker for academic use, or purchase a license.">value</validator>
</param>

<param name="genome" type="data" format="fasta" label="Genome to annotate"/>
<param name="organism_type" type="select" label="Organism type">
<option value="eukaryotic">Eukaryotic</option>
Expand Down Expand Up @@ -302,49 +308,45 @@ TMP= # specify a directory other than the system default temporary directory for
<option value="human">Homo sapiens</option>
<option value="fly">Drosophila melanogaster</option>
<option value="arabidopsis">Arabidopsis thaliana</option>
<option value="brugia ">Brugia malayi</option>
<option value="aedes">Aedes aegypti</option>
<option value="tribolium2012">Tribolium castaneum</option>
<option value="schistosoma">Schistosoma mansoni</option>
<option value="tetrahymena">Tetrahymena thermophila</option>
<option value="galdieria">Galdieria sulphuraria</option>
<option value="maize">Zea mays</option>
<option value="toxoplasma">Toxoplasma gondii</option>
<option value="caenorhabditis ">Caenorhabditis elegans</option>
<option value="caenorhabditis">Caenorhabditis elegans</option>
<option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
<option value="aspergillus_nidulans ">Aspergillus nidulans</option>
<option value="aspergillus_oryzae ">Aspergillus oryzae</option>
<option value="aspergillus_nidulans">Aspergillus nidulans</option>
<option value="aspergillus_oryzae">Aspergillus oryzae</option>
<option value="aspergillus_terreus">Aspergillus terreus</option>
<option value="botrytis_cinerea ">Botrytis cinerea</option>
<option value="candida_albicans ">Candida albicans</option>
<option value="candida_guilliermondii ">Candida guilliermondii</option>
<option value="candida_tropicalis ">Candida tropicalis</option>
<option value="botrytis_cinerea">Botrytis cinerea</option>
<option value="candida_albicans">Candida albicans</option>
<option value="candida_guilliermondii">Candida guilliermondii</option>
<option value="candida_tropicalis">Candida tropicalis</option>
<option value="chaetomium_globosum">Chaetomium globosum</option>
<option value="coccidioides_immitis">Coccidioides immitis</option>
<option value="coprinus">Coprinus cinereus</option>
<option value="coprinus_cinereus">Coprinus cinereus</option>
<option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
<option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
<option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
<option value="cryptococcus">Cryptococcus neoformans</option>
<option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
<option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
<option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
<option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
<option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
<option value="eremothecium_gossypii">Eremothecium gossypii</option>
<option value="fusarium_graminearum ">Fusarium graminearum</option>
<option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
<option value="histoplasma">Histoplasma capsulatum</option>
<option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
<option value="laccaria_bicolor ">Laccaria bicolor</option>
<option value="fusarium_graminearum">Fusarium graminearum</option>
<option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
<option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
<option value="laccaria_bicolor">Laccaria bicolor</option>
<option value="lamprey">Petromyzon marinus</option>
<option value="leishmania_tarentolae">Leishmania tarentolae</option>
<option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
<option value="magnaporthe_grisea ">Magnaporthe grisea</option>
<option value="magnaporthe_grisea">Magnaporthe grisea</option>
<option value="neurospora_crassa">Neurospora crassa</option>
<option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
<option value="pichia_stipitis">Pichia stipitis</option>
<option value="rhizopus_oryzae">Rhizopus oryzae</option>
<option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
<option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
<option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
<option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a_1</option>
<option value="saccharomyces">Saccharomyces cerevisiae</option>
<option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
<option value="trichinella">Trichinella spiralis</option>
Expand All @@ -367,25 +369,21 @@ TMP= # specify a directory other than the system default temporary directory for
<option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
<option value="wheat">wheat</option>
<option value="zebrafish">Danio rerio</option>
<option value="anidulans">Aspergillus nidulans</option>
<option value="bombus_impatiens1">Bombus impatiens1</option>
<option value="bombus_terrestris2">Bombus terrestris2</option>
<option value="botrytis_cinerea">Botrytis cinerea</option>
<option value="brugia_malayi">Brugia malayi</option>
<option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
<option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
<option value="culex_pipiens">Culex pipiens</option>
<option value="elephant_shark">Callorhinchus milii</option>
<option value="honeybee1">Apis mellifera</option>
<option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
<option value="pea_aphid">Acyrthosiphon pisum</option>
<option value="rhodnius_prolixus">Rhodnius prolixus</option>
<option value="ustilago_maydis">Ustilago maydis</option>
<option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
<option value="verticillium_longisporum1">Verticillium longisporum1</option>
<option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
<option value="Xipophorus_maculatus">Xipophorus maculatus</option>
<option value="adorsata">adorsata</option>
<option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
<option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
<option value="maker2_athal1">maker2_athal1</option>
<option value="maker2_c_elegans1">maker2_c_elegans1</option>
<option value="maker2_dmel1">maker2_dmel1</option>
Expand Down Expand Up @@ -492,6 +490,7 @@ TMP= # specify a directory other than the system default temporary directory for
</outputs>
<tests>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="est_evidences|est" value="est.fasta"/>
<param name="est_evidences|est2genome" value="1"/>
Expand All @@ -500,6 +499,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="organism_type" value="prokaryotic"/>
<param name="est_evidences|est" value="est.fasta"/>
Expand All @@ -509,6 +509,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="reannotation|reannotate" value="yes"/>
<param name="reannotation|maker_gff" value="evidences.gff3"/>
Expand All @@ -519,6 +520,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
<param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="builtin"/>
Expand All @@ -530,6 +532,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
<param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="history"/>
Expand All @@ -541,6 +544,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="est_evidences|est" value="est.fasta"/>
<param name="est_evidences|est2genome" value="1"/>
Expand All @@ -549,6 +553,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="est_evidences|est" value="est.fasta"/>
<param name="est_evidences|est2genome" value="1"/>
Expand All @@ -558,6 +563,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="est_evidences|est" value="est.fasta"/>
<param name="est_evidences|est2genome" value="1"/>
Expand All @@ -568,6 +574,7 @@ TMP= # specify a directory other than the system default temporary directory for
<output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
</test>
<test>
<param name="license_agreement" value="true" />
<param name="genome" value="genome.fasta"/>
<param name="est_evidences|est" value="non_IUPAC.fasta"/>
<param name="est_evidences|est2genome" value="1"/>
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