diff ProteinResolver.xml @ 13:851f7c252d66 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- 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>