diff NovorAdapter.xml @ 0:562d46a2f8b6 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NovorAdapter.xml	Thu Aug 27 19:40:35 2020 -0400
@@ -0,0 +1,167 @@
+<?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="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+  <description>Template for Tool creation</description>
+  <macros>
+    <token name="@EXECUTABLE@">NovorAdapter</token>
+    <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+#if $novorFile:
+  mkdir novorFile &&
+  ln -s '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
+#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("idxml")}'
+#if $novorFile:
+  -novorFile
+  'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)'
+#end if
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "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="MzML Input file" help=" select mzml data sets(s)"/>
+    <param name="enzyme" argument="-enzyme" display="radio" type="select" optional="false" label="Digestion enzyme - currently only Trypsin is supported" help="">
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="fragmentation" argument="-fragmentation" display="radio" type="select" optional="false" label="Fragmentation method" help="">
+      <option value="CID" selected="true">CID</option>
+      <option value="HCD">HCD</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="massAnalyzer" argument="-massAnalyzer" display="radio" type="select" optional="false" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
+      <option value="Trap" selected="true">Trap</option>
+      <option value="TOF">TOF</option>
+      <option value="FT">FT</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
+    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
+    <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
+      <option value="ppm" selected="true">ppm</option>
+      <option value="Da">Da</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help="">
+      <option value="">default (nothing chosen)</option>
+      <option value="Acetyl (K)">Acetyl (K)</option>
+      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
+      <option value="Amidated (C-term)">Amidated (C-term)</option>
+      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
+      <option value="Biotin (K)">Biotin (K)</option>
+      <option value="Biotin (N-term)">Biotin (N-term)</option>
+      <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
+      <option value="Carbamyl (K)">Carbamyl (K)</option>
+      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
+      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
+      <option value="Deamidated (NQ)">Deamidated (NQ)</option>
+      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
+      <option value="Dioxidation (M)">Dioxidation (M)</option>
+      <option value="Methyl (C-term)">Methyl (C-term)</option>
+      <option value="Methyl (DE)">Methyl (DE)</option>
+      <option value="Oxidation (M)">Oxidation (M)</option>
+      <option value="Oxidation (HW)">Oxidation (HW)</option>
+      <option value="Phospho (ST)">Phospho (ST)</option>
+      <option value="Phospho (Y)">Phospho (Y)</option>
+      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
+      <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
+      <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
+      <option value="Sodium (C-term)">Sodium (C-term)</option>
+      <option value="Sodium (DE)">Sodium (DE)</option>
+      <option value="Sulfo (STY)">Sulfo (STY)</option>
+      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="fixed_modifications" argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help="">
+      <option value="">default (nothing chosen)</option>
+      <option value="Acetyl (K)">Acetyl (K)</option>
+      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
+      <option value="Amidated (C-term)">Amidated (C-term)</option>
+      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
+      <option value="Biotin (K)">Biotin (K)</option>
+      <option value="Biotin (N-term)">Biotin (N-term)</option>
+      <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
+      <option value="Carbamyl (K)">Carbamyl (K)</option>
+      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
+      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
+      <option value="Deamidated (NQ)">Deamidated (NQ)</option>
+      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
+      <option value="Dioxidation (M)">Dioxidation (M)</option>
+      <option value="Methyl (C-term)">Methyl (C-term)</option>
+      <option value="Methyl (DE)">Methyl (DE)</option>
+      <option value="Oxidation (M)">Oxidation (M)</option>
+      <option value="Oxidation (HW)">Oxidation (HW)</option>
+      <option value="Phospho (ST)">Phospho (ST)</option>
+      <option value="Phospho (Y)">Phospho (Y)</option>
+      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
+      <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
+      <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
+      <option value="Sodium (C-term)">Sodium (C-term)</option>
+      <option value="Sodium (DE)">Sodium (DE)</option>
+      <option value="Sulfo (STY)">Sulfo (STY)</option>
+      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="forbiddenResidues" argument="-forbiddenResidues" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
+      <option value="">default (nothing chosen)</option>
+      <option value="I">I</option>
+      <option value="U">U</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="novorFile" argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests>
+    <expand macro="autotest_NovorAdapter"/>
+    <expand macro="manutest_NovorAdapter"/>
+  </tests>
+  <help><![CDATA[Template for Tool creation
+
+
+For more information, visit http://www.openms.de/documentation/UTILS_NovorAdapter.html]]></help>
+  <expand macro="references"/>
+</tool>