diff MultiplexResolver.xml @ 13:021fdb80f204 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:58 +0000
parents b3dcd2098472
children 53b202a738c3
line wrap: on
line diff
--- a/MultiplexResolver.xml	Fri Nov 06 20:28:49 2020 +0000
+++ b/MultiplexResolver.xml	Thu Dec 01 19:14:58 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: [Utilities]-->
-<tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Completes peptide multiplets and resolves conflicts within them.</description>
   <macros>
     <token name="@EXECUTABLE@">MultiplexResolver</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -62,11 +60,11 @@
     <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="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
-    <param name="in_blacklist" argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
     <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
-      <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. . [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
-        <expand macro="list_string_san"/>
+      <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example.  [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
+        <expand macro="list_string_san" name="labels"/>
       </param>
       <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
       <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
@@ -90,9 +88,9 @@
       <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help=""/>
     </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">
@@ -109,13 +107,167 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MultiplexResolver"/>
-    <expand macro="manutest_MultiplexResolver"/>
+  <tests><!-- UTILS_MultiplexResolver_1 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
+      <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <section name="algorithm">
+        <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
+        <param name="missed_cleavages" value="1"/>
+        <param name="mass_tolerance" value="0.1"/>
+        <param name="mz_tolerance" value="10"/>
+        <param name="rt_tolerance" value="5"/>
+      </section>
+      <section name="labels">
+        <param name="Arg6" value="6.0201290268"/>
+        <param name="Arg10" value="10.0082686"/>
+        <param name="Lys4" value="4.0251069836"/>
+        <param name="Lys6" value="6.0201290268"/>
+        <param name="Lys8" value="8.0141988132"/>
+        <param name="Leu3" value="3.01883"/>
+        <param name="Dimethyl0" value="28.0313"/>
+        <param name="Dimethyl4" value="32.056407"/>
+        <param name="Dimethyl6" value="34.063117"/>
+        <param name="Dimethyl8" value="36.07567"/>
+        <param name="ICPL0" value="105.021464"/>
+        <param name="ICPL4" value="109.046571"/>
+        <param name="ICPL6" value="111.041593"/>
+        <param name="ICPL10" value="115.0667"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_MultiplexResolver_2 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
+      <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <section name="algorithm">
+        <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
+        <param name="missed_cleavages" value="4"/>
+        <param name="mass_tolerance" value="0.1"/>
+        <param name="mz_tolerance" value="10"/>
+        <param name="rt_tolerance" value="5"/>
+      </section>
+      <section name="labels">
+        <param name="Arg6" value="6.0201290268"/>
+        <param name="Arg10" value="10.0082686"/>
+        <param name="Lys4" value="4.0251069836"/>
+        <param name="Lys6" value="6.0201290268"/>
+        <param name="Lys8" value="8.0141988132"/>
+        <param name="Leu3" value="3.01883"/>
+        <param name="Dimethyl0" value="28.0313"/>
+        <param name="Dimethyl4" value="32.056407"/>
+        <param name="Dimethyl6" value="34.063117"/>
+        <param name="Dimethyl8" value="36.07567"/>
+        <param name="ICPL0" value="105.021464"/>
+        <param name="ICPL4" value="109.046571"/>
+        <param name="ICPL6" value="111.041593"/>
+        <param name="ICPL10" value="115.0667"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_MultiplexResolver_3 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
+      <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <section name="algorithm">
+        <param name="labels" value="[][Leu3]"/>
+        <param name="missed_cleavages" value="2"/>
+        <param name="mass_tolerance" value="0.1"/>
+        <param name="mz_tolerance" value="10"/>
+        <param name="rt_tolerance" value="5"/>
+      </section>
+      <section name="labels">
+        <param name="Arg6" value="6.0201290268"/>
+        <param name="Arg10" value="10.0082686"/>
+        <param name="Lys4" value="4.0251069836"/>
+        <param name="Lys6" value="6.0201290268"/>
+        <param name="Lys8" value="8.0141988132"/>
+        <param name="Leu3" value="3.01883"/>
+        <param name="Dimethyl0" value="28.0313"/>
+        <param name="Dimethyl4" value="32.056407"/>
+        <param name="Dimethyl6" value="34.063117"/>
+        <param name="Dimethyl8" value="36.07567"/>
+        <param name="ICPL0" value="105.021464"/>
+        <param name="ICPL4" value="109.046571"/>
+        <param name="ICPL6" value="111.041593"/>
+        <param name="ICPL10" value="115.0667"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_MultiplexResolver_4 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
+      <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
+      <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <section name="algorithm">
+        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
+        <param name="missed_cleavages" value="3"/>
+        <param name="mass_tolerance" value="0.1"/>
+        <param name="mz_tolerance" value="10"/>
+        <param name="rt_tolerance" value="10"/>
+      </section>
+      <section name="labels">
+        <param name="Arg6" value="6.0201290268"/>
+        <param name="Arg10" value="10.0082686"/>
+        <param name="Lys4" value="4.0251069836"/>
+        <param name="Lys6" value="6.0201290268"/>
+        <param name="Lys8" value="8.0141988132"/>
+        <param name="Leu3" value="3.01883"/>
+        <param name="Dimethyl0" value="28.0313"/>
+        <param name="Dimethyl4" value="32.056407"/>
+        <param name="Dimethyl6" value="34.063117"/>
+        <param name="Dimethyl8" value="36.07567"/>
+        <param name="ICPL0" value="105.021464"/>
+        <param name="ICPL4" value="109.046571"/>
+        <param name="ICPL6" value="111.041593"/>
+        <param name="ICPL10" value="115.0667"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MultiplexResolver.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MultiplexResolver.html]]></help>
   <expand macro="references"/>
 </tool>