| Previous changeset 8:3c1a01127868 (2021-06-28) Next changeset 10:370c210d9541 (2022-08-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 739da8be15072cfd98cc0b8d6bfa9dedb25a98f0" |
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modified:
macros.xml maker.xml |
| b |
| diff -r 3c1a01127868 -r a444254e9a57 macros.xml --- a/macros.xml Mon Jun 28 09:40:12 2021 +0000 +++ b/macros.xml Tue Feb 08 14:17:58 2022 +0000 |
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| @@ -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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| diff -r 3c1a01127868 -r a444254e9a57 maker.xml --- a/maker.xml Mon Jun 28 09:40:12 2021 +0000 +++ b/maker.xml Tue Feb 08 14:17:58 2022 +0000 |
| [ |
| b'@@ -4,6 +4,9 @@\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">maker</xref>\n+ </xrefs>\n <expand macro="requirements"/>\n <command><![CDATA[\n RM_PATH=\\$(which RepeatMasker) &&\n@@ -242,6 +245,12 @@\n </configfiles>\n \n <inputs>\n+ <!-- More info on licensing in https://github.com/galaxyproject/iwc/pull/47#issuecomment-962260646 -->\n+ <param name="license_agreement" type="boolean" label="Are you running Maker for academic use, or did you purchase a license?"\n+ 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">\n+ <validator type="expression" message="You must either run Maker for academic use, or purchase a license.">value</validator>\n+ </param>\n+\n <param name="genome" type="data" format="fasta" label="Genome to annotate"/>\n <param name="organism_type" type="select" label="Organism type">\n <option value="eukaryotic">Eukaryotic</option>\n@@ -299,7 +308,6 @@\n <option value="human">Homo sapiens</option>\n <option value="fly">Drosophila melanogaster</option>\n <option value="arabidopsis">Arabidopsis thaliana</option>\n- <option value="brugia ">Brugia malayi</option>\n <option value="aedes">Aedes aegypti</option>\n <option value="tribolium2012">Tribolium castaneum</option>\n <option value="schistosoma">Schistosoma mansoni</option>\n@@ -307,41 +315,38 @@\n <option value="galdieria">Galdieria sulphuraria</option>\n <option value="maize">Zea mays</option>\n <option value="toxoplasma">Toxoplasma gondii</option>\n- <option value="caenorhabditis ">Caenorhabditis elegans</option>\n+ <option value="caenorhabditis">Caenorhabditis elegans</option>\n <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>\n- <option value="aspergillus_nidulans ">Aspergillus nidulans</option>\n- <option value="aspergillus_oryzae ">Aspergillus oryzae</option>\n+ <option value="aspergillus_nidulans">Aspergillus nidulans</option>\n+ <option value="aspergillus_oryzae">Aspergillus oryzae</option>\n <option value="aspergillus_terreus">Aspergillus terreus</option>\n- <option value="botrytis_cinerea ">Botrytis cinerea</option>\n- <option value="candida_albicans ">Candida albicans</option>\n- <option value="candida_guilliermondii ">Candida guilliermondii</option>\n- <option value="candida_tropicalis ">Candida tropicalis</option>\n+ <option value="botrytis_cinerea">Botrytis cinerea</option>\n+ <option value="candida_albicans">Candida albicans</option>\n+ <option value="candida_guilliermondii">Candida guilliermondii</option>\n+ <option value="candida_tropicalis">Candida tropicalis</option>\n <option value="chaetomium_globosum">Chaetomium globosum</option>\n <option value="coccidioides_immitis">Coccidioides immitis</option>\n- <option value="coprinus">Coprinus cinereus</option>\n <option value="coprinus_cinereus">Coprinus cinereus</option>\n <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>\n- <option value="cryptococcus_neoformans_neoformans_B">Cryptoc'..b' <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>\n+ <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>\n <option value="maker2_athal1">maker2_athal1</option>\n <option value="maker2_c_elegans1">maker2_c_elegans1</option>\n <option value="maker2_dmel1">maker2_dmel1</option>\n@@ -489,6 +490,7 @@\n </outputs>\n <tests>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n@@ -497,6 +499,7 @@\n <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="organism_type" value="prokaryotic"/>\n <param name="est_evidences|est" value="est.fasta"/>\n@@ -506,6 +509,7 @@\n <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="reannotation|reannotate" value="yes"/>\n <param name="reannotation|maker_gff" value="evidences.gff3"/>\n@@ -516,6 +520,7 @@\n <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>\n <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="builtin"/>\n@@ -527,6 +532,7 @@\n <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>\n <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="history"/>\n@@ -538,6 +544,7 @@\n <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n@@ -546,6 +553,7 @@\n <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n@@ -555,6 +563,7 @@\n <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n@@ -565,6 +574,7 @@\n <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>\n </test>\n <test>\n+ <param name="license_agreement" value="true" />\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="non_IUPAC.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n' |