Mercurial > repos > bgruening > repeat_masker
diff repeatmasker.xml @ 11:72aade318318 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit c4bf14b461856220df4b4bbdbb4b9bbad1ff8749"
author | iuc |
---|---|
date | Thu, 20 May 2021 12:56:42 +0000 |
parents | bfc70c8cc5ca |
children | 39b40a9a6296 |
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--- a/repeatmasker.xml Fri Dec 11 22:26:02 2020 +0000 +++ b/repeatmasker.xml Thu May 20 12:56:42 2021 +0000 @@ -1,11 +1,13 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01"> - <description>screen DNA sequences for interspersed repeats and low complexity regions</description> - - <requirements> - <requirement type="package" version="4.1.1">repeatmasker</requirement> - </requirements> - - <command detect_errors="exit_code"><![CDATA[ +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01"> + <description>screen DNA sequences for interspersed repeats and low complexity regions</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro='edam_ontology' /> + <expand macro='requirements' /> + <version_command>repeatmasker --version</version_command> + <command detect_errors="exit_code"><![CDATA[ RM_PATH=\$(which RepeatMasker) && if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && @@ -97,12 +99,10 @@ </param> <when value="yes"> <param name="species_list" type="select" label="Species"> - <option value="vertebrate">Vertebrate (other than below)</option> - <option value="mammal">Mammal (other than below)</option> - <option value="human" selected="true">Human</option> - <option value="rodent">Rodent</option> - <option value="mouse">Mouse</option> - <option value="rat">Rat</option> + <option value="human" selected="true">Human (Homo sapiens)</option> + <option value="rodent">Rodent (Order Rodentia)</option> + <option value="mouse">Mouse (Mus musculus)</option> + <option value="rattus">Rat (Rattus sp.)</option> <option value="danio">Danio (zebra fish)</option> <option value="drosophila">Fruit fly (Drosophila melanogaster)</option> <option value="elegans">Caenorhabditis elegans (nematode)</option> @@ -219,6 +219,15 @@ <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" /> <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/> </test> + <test expect_num_outputs="4"> + <param name="input_fasta" value="small.fasta" ftype="fasta" /> + <param name="source_type" value="dfam" /> + <param name="species_list" value="rattus" /> + <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" /> + <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" /> + <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" /> + <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/> + </test> </tests> <help><![CDATA[ RepeatMasker is a program that screens DNA for interspersed repeats and low @@ -234,13 +243,5 @@ .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html ]]> </help> - <citations> - <citation type="bibtex"> - @misc{RepeatMasker, - title = {RepeatMasker Open-4.0}, - howpublished = {\url{http://www.repeatmasker.org}}, - author = {Smit, AFA and Hubley, R and Green, P.}, - year = {2013-2015}} - </citation> - </citations> + <expand macro="citations" /> </tool>