diff CompNovo.xml @ 16:cd9449dbe4e4 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:17:28 +0000
parents 3a8e53c6b9d6
children
line wrap: on
line diff
--- a/CompNovo.xml	Fri Nov 06 20:05:59 2020 +0000
+++ b/CompNovo.xml	Thu Dec 01 19:17:28 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: [Identification]-->
-<tool id="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Performs a de novo peptide identification using the CompNovo engine.</description>
   <macros>
     <token name="@EXECUTABLE@">CompNovo</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,12 +39,10 @@
     <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="mzml" optional="false" label="input file in mzML format" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm section" help="" expanded="false">
       <param name="max_number_aa_per_decomp" argument="-algorithm:max_number_aa_per_decomp" type="integer" optional="true" value="4" label="maximal amino acid frequency per decomposition" help=""/>
-      <param name="tryptic_only" argument="-algorithm:tryptic_only" type="text" optional="true" value="true" label="if set to true only tryptic peptides are reported" help="">
-        <expand macro="list_string_san"/>
-      </param>
+      <param name="tryptic_only" argument="-algorithm:tryptic_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="if set to true only tryptic peptides are reported" help=""/>
       <param name="precursor_mass_tolerance" argument="-algorithm:precursor_mass_tolerance" type="float" optional="true" value="1.5" label="precursor mass tolerance" help=""/>
       <param name="fragment_mass_tolerance" argument="-algorithm:fragment_mass_tolerance" type="float" optional="true" value="0.3" label="fragment mass tolerance" help=""/>
       <param name="max_number_pivot" argument="-algorithm:max_number_pivot" type="integer" optional="true" value="9" label="maximal number of pivot ions to be used" help=""/>
@@ -63,7 +59,6 @@
       <param name="estimate_precursor_mz" argument="-algorithm:estimate_precursor_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true, the precursor charge will be estimated" help="e.g. from the precursor peaks of the ETD spectrum.. The input is believed otherwise"/>
       <param name="number_of_prescoring_hits" argument="-algorithm:number_of_prescoring_hits" type="integer" optional="true" value="250" label="how many sequences are kept after first rough scoring for better scoring" help=""/>
       <param name="fixed_modifications" argument="-algorithm:fixed_modifications" multiple="true" type="select" optional="true" label="fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-        <option value="">default (nothing chosen)</option>
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -1433,7 +1428,6 @@
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
@@ -2992,10 +2986,9 @@
         <option value="ZGB (K)">ZGB (K)</option>
         <option value="ZGB (N-term)">ZGB (N-term)</option>
         <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="fixed_modifications"/>
       </param>
       <param name="variable_modifications" argument="-algorithm:variable_modifications" multiple="true" type="select" optional="true" label="variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-        <option value="">default (nothing chosen)</option>
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -4365,7 +4358,6 @@
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
@@ -5924,16 +5916,16 @@
         <option value="ZGB (K)">ZGB (K)</option>
         <option value="ZGB (N-term)">ZGB (N-term)</option>
         <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="variable_modifications"/>
       </param>
       <param name="residue_set" argument="-algorithm:residue_set" type="text" optional="true" value="Natural19WithoutI" label="The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets" help="">
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="residue_set"/>
       </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">
@@ -5946,13 +5938,47 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_CompNovo"/>
-    <expand macro="manutest_CompNovo"/>
+  <tests><!-- TOPP_CompNovo_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="CompNovo_1_input.mzML"/>
+      <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <section name="algorithm">
+        <param name="max_number_aa_per_decomp" value="4"/>
+        <param name="tryptic_only" value="true"/>
+        <param name="precursor_mass_tolerance" value="0.3"/>
+        <param name="fragment_mass_tolerance" value="0.3"/>
+        <param name="max_number_pivot" value="9"/>
+        <param name="max_subscore_number" value="40"/>
+        <param name="decomp_weights_precision" value="0.01"/>
+        <param name="double_charged_iso_threshold" value="0.6"/>
+        <param name="max_mz" value="2000.0"/>
+        <param name="min_mz" value="200.0"/>
+        <param name="max_isotope_to_score" value="3"/>
+        <param name="max_decomp_weight" value="450.0"/>
+        <param name="max_isotope" value="3"/>
+        <param name="missed_cleavages" value="1"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="estimate_precursor_mz" value="true"/>
+        <param name="number_of_prescoring_hits" value="250"/>
+        <param name="fixed_modifications"/>
+        <param name="variable_modifications"/>
+        <param name="residue_set" value="Natural19WithoutI"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Performs a de novo peptide identification using the CompNovo engine.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CompNovo.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CompNovo.html]]></help>
   <expand macro="references"/>
 </tool>