Mercurial > repos > galaxyp > openms_proteinresolver
diff ProteinResolver.xml @ 13:851f7c252d66 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 18:57:06 +0000 |
parents | 95f90fab5ce8 |
children | c2612cb89529 |
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--- a/ProteinResolver.xml Fri Nov 06 20:42:14 2020 +0000 +++ b/ProteinResolver.xml Thu Dec 01 18:57:06 2022 +0000 @@ -1,13 +1,11 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Quantitation]--> -<tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>protein inference</description> <macros> <token name="@EXECUTABLE@">ProteinResolver</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -18,9 +16,14 @@ ## Preprocessing mkdir fasta && ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && -#if $in: - mkdir in && - ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +#if $in_cond.in: + mkdir in_cond.in && + #if $in_cond.in_select == "no" + mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && + ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} + #else + ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && + #end if #end if #if $design: mkdir design && @@ -47,9 +50,13 @@ @EXECUTABLE@ -ini @EXECUTABLE@.ctd -fasta 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' -#if $in: +#if $in_cond.in: -in - ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} + #if $in_cond.in_select == "no" + ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} + #else + 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' + #end if #end if #if $design: -design @@ -96,39 +103,50 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="fasta" argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/> - <param name="in" argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> - <param name="in_path" argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given"> - <expand macro="list_string_san"/> + <param argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/> + <conditional name="in_cond"> + <param name="in_select" type="select" label="Run tool in batch mode for -in"> + <option value="no">No: process all datasets jointly</option> + <option value="yes">Yes: process each dataset in an independent job</option> + </param> + <when value="no"> + <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> + </when> + <when value="yes"> + <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> + </when> + </conditional> + <param argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given"> + <expand macro="list_string_san" name="in_path"/> </param> - <param name="design" argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/> + <param argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/> <section name="resolver" title="Additional options for algorithm" help="" expanded="false"> <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/> <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/> - <param name="enzyme" argument="-resolver:enzyme" display="radio" type="select" optional="false" label="Digestion enzyme" help=""> + <param name="enzyme" argument="-resolver:enzyme" type="select" optional="true" label="Digestion enzyme" help=""> <option value="Trypsin" selected="true">Trypsin</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="enzyme"/> </param> </section> <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false"> <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="experiment"/> </param> <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="file"/> </param> - <param name="separator" argument="-designer:separator" display="radio" type="select" optional="false" label="Separator, which should be used to split a row into columns" help=""> + <param name="separator" argument="-designer:separator" type="select" optional="true" label="Separator, which should be used to split a row into columns" help=""> <option value="tab" selected="true">tab</option> <option value="semi-colon">semi-colon</option> <option value="comma">comma</option> <option value="whitespace">whitespace</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="separator"/> </param> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -159,13 +177,41 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_ProteinResolver"/> - <expand macro="manutest_ProteinResolver"/> + <tests><!-- TOPP_ProteinResolver_1 --> + <test expect_num_outputs="4"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="fasta" value="ProteinResolver_1_input.fasta"/> + <conditional name="in_cond"> + <param name="in" value="ProteinResolver_1_input.consensusXML"/> + </conditional> + <param name="in_path" value=""/> + <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <section name="resolver"> + <param name="missed_cleavages" value="2"/> + <param name="min_length" value="6"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="designer"> + <param name="experiment" value="ExperimentalSetting"/> + <param name="file" value="File"/> + <param name="separator" value="tab"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[protein inference -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ProteinResolver.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinResolver.html]]></help> <expand macro="references"/> </tool>