Mercurial > repos > galaxyp > openms_falsediscoveryrate

diff FalseDiscoveryRate.xml @ 16:4138acdeedfb draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:39:03 +0000
parents 6ccbf9a2072c
children
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--- a/FalseDiscoveryRate.xml	Thu Dec 01 19:02:41 2022 +0000
+++ b/FalseDiscoveryRate.xml	Fri Jun 14 21:39:03 2024 +0000
@@ -1,8 +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 CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
+  <description>Estimates the false discovery rate on peptide and protein level using decoy searches</description>
   <macros>
     <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,12 +38,13 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
     <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
+    <param argument="-peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform FDR calculation on peptide level and annotates it as meta value" help="(Note: if set, also calculates FDR/q-value on PSM level.)"/>
     <param argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
     <section name="FDR" title="FDR control" help="" expanded="false">
-      <param name="PSM" argument="-FDR:PSM" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
-      <param name="protein" argument="-FDR:protein" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
+      <param name="PSM" argument="-FDR:PSM" type="float" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
+      <param name="protein" argument="-FDR:protein" type="float" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
       <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
         <param name="remove_proteins_without_psms" argument="-FDR:cleanup:remove_proteins_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove proteins without PSMs (due to being decoy or below PSM FDR threshold)" help=""/>
         <param name="remove_psms_without_proteins" argument="-FDR:cleanup:remove_psms_without_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove PSMs without proteins (due to being decoy or below protein FDR threshold)" help=""/>
@@ -62,7 +62,7 @@
     </section>
     <expand macro="adv_opts_macro">
       <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="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -76,15 +76,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FalseDiscoveryRate_1 -->
+  <tests>
+    <!-- TOPP_FalseDiscoveryRate_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -110,6 +112,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_2 -->
     <test expect_num_outputs="2">
@@ -118,8 +123,9 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -145,6 +151,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_3 -->
     <test expect_num_outputs="2">
@@ -153,8 +162,9 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -180,6 +190,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_4 -->
     <test expect_num_outputs="2">
@@ -188,8 +201,9 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -215,6 +229,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_5 -->
     <test expect_num_outputs="2">
@@ -223,8 +240,9 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="false"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="true"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -250,6 +268,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_6 -->
     <test expect_num_outputs="2">
@@ -258,8 +279,9 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="0.05"/>
@@ -285,6 +307,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_7 -->
     <test expect_num_outputs="2">
@@ -293,8 +318,9 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="false"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="true"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -320,11 +346,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FalseDiscoveryRate.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FalseDiscoveryRate.html]]></help>
   <expand macro="references"/>
 </tool>