diff pepquery2_index.xml @ 0:e9ef3add4ca8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pepquery2_index.xml	Wed Sep 28 13:56:39 2022 +0000
@@ -0,0 +1,50 @@
+<tool id="pepquery2_index" name="PepQuery index" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+    <description>MS/MS data for faster search</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+@CMD_IMPORTS@
+@INDEX_SPECTRUM_FILES@
+$index_spectrum_files($output.files_path, $inputs)
+    ]]></command>
+    <inputs>
+        <param name="inputs" argument="-i" type="data" format="mfg,mzml,mzxml" multiple="true" label="MS Spectrum files">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} on ${on_string}: summary.txt" from_work_dir="index_dir/summary.txt"/> 
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" ftype="mzml" value="small-index-filter.mzML"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="small-index-filter.mzML"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs" value="small-index-filter.mzML,AgilentMassHunterTest.mzXML,immunopeptidomics.mgf"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="small-index-filter.mzML"/>
+                    <has_text text="AgilentMassHunterTest.mzXML"/>
+                    <has_text text="immunopeptidomics.mgf"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**PepQuery Index** 
+
+Indexes MS/MS data for fast searching.  
+This can significant speed up the search especially when the size of MS/MS data is very large.
+
+The output can be used as input to **PepQuery2** Galaxy tool in the **MS/MS dataset to search** *Indexed MS/MS spectrums*.
+    ]]></help>
+    <expand macro="citations" />
+</tool>