diff IDFileConverter.xml @ 3:066cf4d993f5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:10:41 -0400
parents 5588e443a7db
children 1dcffdad49c0
line wrap: on
line diff
--- a/IDFileConverter.xml	Thu Apr 27 13:23:15 2017 -0400
+++ b/IDFileConverter.xml	Wed Aug 09 09:10:41 2017 -0400
@@ -1,7 +1,7 @@
 <?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 CTD2Galaxy.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="IDFileConverter" name="IDFileConverter" version="2.1.0">
+<tool id="IDFileConverter" name="IDFileConverter" version="2.2.0">
   <description>Converts identification engine file formats.</description>
   <macros>
     <token name="@EXECUTABLE@">IDFileConverter</token>
@@ -11,68 +11,71 @@
   <expand macro="stdio"/>
   <expand macro="requirements"/>
   <command><![CDATA[
-   
-  ## check input file type
-  #set $in_type = $param_in.ext
+
+## check input file type
+#set $in_type = $param_in.ext
 
-  ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
-  ln -s '$param_in' 'param_in.${in_type}' &&
-  
-  IDFileConverter
+## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+ln -s '$param_in' 'param_in.${in_type}' &&
+
+IDFileConverter
 
-  #if $param_in:
-    -in 'param_in.${in_type}'
-  #end if
-  #if $param_out:
-    -out $param_out
-  #end if
-  #if $param_out_type:
-    -out_type
-    #if " " in str($param_out_type):
-      "$param_out_type"
-    #else
-      $param_out_type
-    #end if
-  #end if
-  #if $param_mz_file:
-    -mz_file $param_mz_file
+#if $param_in:
+  -in 'param_in.${in_type}'
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_type:
+  -out_type
+  #if " " in str($param_out_type):
+    "$param_out_type"
+  #else
+    $param_out_type
   #end if
-  #if $param_mz_name:
-    -mz_name     "$param_mz_name"
-  #end if
-  #if $param_peptideprophet_analyzed:
-    -peptideprophet_analyzed
+#end if
+#if $param_mz_file:
+  -mz_file $param_mz_file
+#end if
+#if $param_mz_name:
+  -mz_name     "$param_mz_name"
+#end if
+#if $param_peptideprophet_analyzed:
+  -peptideprophet_analyzed
+#end if
+#if $param_score_type:
+  -score_type
+  #if " " in str($param_score_type):
+    "$param_score_type"
+  #else
+    $param_score_type
   #end if
-  #if $param_score_type:
-    -score_type
-    #if " " in str($param_score_type):
-      "$param_score_type"
-    #else
-      $param_score_type
-    #end if
-  #end if
-  #if $adv_opts.adv_opts_selector=='advanced':
-      #if $adv_opts.param_ignore_proteins_per_peptide:
-    -ignore_proteins_per_peptide
-  #end if
-      #if $adv_opts.param_scan_regex:
-    -scan_regex     "$adv_opts.param_scan_regex"
-  #end if
-      #if $adv_opts.param_force:
-    -force
-  #end if
-  #end if
- ]]>
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_ignore_proteins_per_peptide:
+  -ignore_proteins_per_peptide
+#end if
+    #if $adv_opts.param_scan_regex:
+  -scan_regex     "$adv_opts.param_scan_regex"
+#end if
+    #if $adv_opts.param_no_spectra_data_override:
+  -no_spectra_data_override
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+]]>
 </command>
   <inputs>
-    <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
+    <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
     <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
       <option value="idXML">idXML</option>
       <option value="mzid">mzid</option>
       <option value="pepXML">pepXML</option>
       <option value="FASTA">FASTA</option>
     </param>
-    <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" help="(-mz_file) "/>
+    <param name="param_mz_file" type="data" format="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file" help="(-mz_file) "/>
     <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'">
       <sanitizer>
         <valid initial="string.printable">
@@ -97,6 +100,7 @@
           </valid>
         </sanitizer>
       </param>
+      <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/>
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
     </expand>
   </inputs>