Mercurial > repos > galaxyp > openms_clustermasstracesbyprecursor

diff ClusterMassTracesByPrecursor.xml @ 5:f0c018228cec 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 21:42:26 +0000
parents 75480fff2586
children
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--- a/ClusterMassTracesByPrecursor.xml	Thu Dec 01 19:22:18 2022 +0000
+++ b/ClusterMassTracesByPrecursor.xml	Fri Jun 14 21:42:26 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: [Utilities]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="ClusterMassTracesByPrecursor" name="ClusterMassTracesByPrecursor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.</description>
+  <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile</description>
   <macros>
     <token name="@EXECUTABLE@">ClusterMassTracesByPrecursor</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in_ms1 &&
-ln -s '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' &&
+cp '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' &&
 mkdir in_swath &&
-ln -s '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' &&
+cp '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,18 +42,18 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_ms1" type="data" format="consensusxml" optional="false" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
-    <param argument="-in_swath" type="data" format="consensusxml" optional="false" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_ms1" type="data" format="consensusxml" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_swath" type="data" format="consensusxml" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
     <param argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/>
-    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
-    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
-    <param argument="-min_nr_ions" type="integer" optional="true" value="3" label="Minimal number of ions to report a spectrum" help=""/>
-    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
-    <param argument="-swath_lower" type="float" optional="true" value="0.0" label="Swath lower isolation window" help=""/>
-    <param argument="-swath_upper" type="float" optional="true" value="0.0" label="Swath upper isolation window" help=""/>
+    <param argument="-min_pearson_correlation" type="float" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
+    <param argument="-max_lag" type="integer" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
+    <param argument="-min_nr_ions" type="integer" value="3" label="Minimal number of ions to report a spectrum" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
+    <param argument="-swath_lower" type="float" value="0.0" label="Swath lower isolation window" help=""/>
+    <param argument="-swath_upper" type="float" value="0.0" label="Swath upper isolation window" help=""/>
     <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>
@@ -68,16 +67,18 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- test with arbitarily chosen consensusXML -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+      <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+      <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
+    </test>
+  </tests>
   <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTracesByPrecursor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ClusterMassTracesByPrecursor.html]]></help>
   <expand macro="references"/>
 </tool>