diff MSstatsConverter.xml @ 0:0dcd11bc33f8 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MSstatsConverter.xml	Wed Sep 09 12:59:06 2020 +0000
@@ -0,0 +1,111 @@
+<?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: [Utilities]-->
+<tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+  <description>Converter to input for MSstats</description>
+  <macros>
+    <token name="@EXECUTABLE@">MSstatsConverter</token>
+    <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir in_design &&
+ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
+mkdir out &&
+#if $adv_opts_cond.adv_opts_selector=='advanced':
+  #if $adv_opts_cond.reannotate_filenames:
+    mkdir adv_opts_cond.reannotate_filenames &&
+    ${ ' '.join(["ln -s '%s' 'adv_opts_cond.reannotate_filenames/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _]) }
+  #end if
+#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-in_design
+'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
+-out
+'out/output.${gxy2omsext("csv")}'
+#if $adv_opts_cond.adv_opts_selector=='advanced':
+  #if $adv_opts_cond.reannotate_filenames:
+    -reannotate_filenames
+    ${' '.join(["'adv_opts_cond.reannotate_filenames/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])}
+  #end if
+#end if
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("csv")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
+    <param name="in_design" argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
+    <param name="method" argument="-method" display="radio" type="select" optional="false" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
+      <option value="LFQ" selected="true">LFQ</option>
+      <option value="ISO">ISO</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="msstats_bioreplicate" argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="msstats_condition" argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="msstats_mixture" argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="labeled_reference_peptides" argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="reannotate_filenames" argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+      <param name="retention_time_summarization_method" argument="-retention_time_summarization_method" type="select" optional="false" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
+        <option value="manual">manual</option>
+        <option value="max" selected="true">max</option>
+        <option value="min">min</option>
+        <option value="mean">mean</option>
+        <option value="sum">sum</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests>
+    <expand macro="autotest_MSstatsConverter"/>
+    <expand macro="manutest_MSstatsConverter"/>
+  </tests>
+  <help><![CDATA[Converter to input for MSstats
+
+
+For more information, visit http://www.openms.de/documentation/UTILS_MSstatsConverter.html]]></help>
+  <expand macro="references"/>
+</tool>