diff OpenMSDatabasesInfo.xml @ 0:a7ff1eeba91f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenMSDatabasesInfo.xml	Thu Dec 01 19:23:33 2022 +0000
@@ -0,0 +1,65 @@
+<?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="OpenMSDatabasesInfo" name="OpenMSDatabasesInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Prints the content of OpenMS' enzyme and modification databases to TSV</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenMSDatabasesInfo</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir enzymes_out &&
+mkdir mods_out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-enzymes_out
+'enzymes_out/output.${gxy2omsext("tabular")}'
+-mods_out
+'mods_out/output.${gxy2omsext("tabular")}'
+
+## Postprocessing
+&& mv 'enzymes_out/output.${gxy2omsext("tabular")}' '$enzymes_out'
+&& mv 'mods_out/output.${gxy2omsext("tabular")}' '$mods_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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <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="">
+        <expand macro="list_string_san" name="test"/>
+      </param>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="enzymes_out" label="${tool.name} on ${on_string}: enzymes_out" format="tabular"/>
+    <data name="mods_out" label="${tool.name} on ${on_string}: mods_out" format="tabular"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Prints the content of OpenMS' enzyme and modification databases to TSV
+
+
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenMSDatabasesInfo.html]]></help>
+  <expand macro="references"/>
+</tool>