# HG changeset patch
# User jjohnson
# Date 1532551558 14400
# Node ID 90dcbb52c83ad24ef36d3cca723bba11de0808cf

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit 225dd7d91b12108dd3a4eec00e45771ec8127259-dirty

diff -r 000000000000 -r 90dcbb52c83a spectrast2spectrast_irt.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast2spectrast_irt.xml	Wed Jul 25 16:45:58 2018 -0400
@@ -0,0 +1,103 @@
+<tool id="gp_spectrast2spectrast_irt" name="SpectraST RT Normalizer" version="0.5.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="0.5.0">msproteomicstools</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+<![CDATA[
+        ## may have to link splib
+        mkdir -p outdir &&
+        spectrast2spectrast_irt.py
+            --in ${input.extra_file_path}/library.sptxt
+            --out outdir/library.splib
+            #if str($kit) != 'None':
+                --kit "#echo ",".join(str($kit).split(','))#"
+            #end if
+            $applychauvenet
+            $precursorlevel
+            $spectralevel
+            $report
+            ##--exclude $exclude
+            ##--surrogate $surrogate
+            ##--linearregression $linearregression
+            --rsq_threshold $rsq_threshold &&
+         cp -p outdir/library.splib outdir/library.sptxt &&
+        mkdir -p '$output.files_path' &&
+        for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done
+]]>
+    </command>
+    <inputs>
+        <param name="input" format="splib" type="data" label="Spectrast files" help="" />
+
+        <param name="applychauvenet" type="boolean" truevalue="--applychauvenet" falsevalue="" checked="False"
+            label="Use Chavenet's criterion to exclude outliers" help="(--applychauvenet)" />
+
+        <param name="precursorlevel" type="boolean" truevalue="--precursorlevel" falsevalue="" checked="False"
+            label="Use precursors instead of peptides for grouping" help="(--precursorlevel)" />
+
+        <param name="spectralevel" type="boolean" truevalue="--spectralevel" falsevalue="" checked="False"
+            label="Do not merge or group any peptides or precursors" help="Use raw spectra. (--spectralevel)" />
+
+        <param name="report" type="boolean" truevalue="--report" falsevalue="" checked="False"
+            label="Create a report CSV file" help="(--report)" />
+
+        <param name="rsq_threshold" type="float" value="0.95" label="Specify r-squared threshold to accept linear regression" help="(--rsq_threshold)" />
+
+        <param name="kit" type="select" multiple="True" optional="True" label="Specifiy RT-kit">
+            <option value="LGGNEQVTR:-28.3083">LGGNEQVTR:-28.3083</option>
+            <option value="GAGSSEPVTGLDAK:0.227424">GAGSSEPVTGLDAK:0.227424</option>
+            <option value="VEATFGVDESNAK:13.1078">VEATFGVDESNAK:13.1078</option>
+            <option value="YILAGVENSK:22.3798">YILAGVENSK:22.3798</option>
+            <option value="TPVISGGPYEYR:28.9999">TPVISGGPYEYR:28.9999</option>
+            <option value="TPVITGAPYEYR:33.6311">TPVITGAPYEYR:33.6311</option>
+            <option value="DGLDAASYYAPVR:43.2819">DGLDAASYYAPVR:43.2819</option>
+            <option value="ADVTPADFSEWSK:54.969">ADVTPADFSEWSK:54.969</option>
+            <option value="GTFIIDPGGVIR:71.3819">GTFIIDPGGVIR:71.3819</option>
+            <option value="GTFIIDPAAVIR:86.7152">GTFIIDPAAVIR:86.7152</option>
+            <option value="LFLQFGAQGSPFLK:98.0897">LFLQFGAQGSPFLK:98.0897</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_report" format="csv" from_work_dir="outdir/library.csv">
+            <filter>report</filter>
+        </data>
+        <data name="output" format="splib"/>
+    </outputs>
+    <tests>
+        <!--
+        <test>
+            <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
+            <param name="report" value="True" />
+            <output name="output_splib" file="spectrast2spectrast_irt_output_1_splib.txt" ftype="txt" />
+            <output name="output_pepidx" file="spectrast2spectrast_irt_output_1_pepids.txt" ftype="txt" />
+            <output name="output_report" file="spectrast2spectrast_irt_output_1_report.txt" ftype="txt" />
+        </test>
+        <test>
+            <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
+            <param name="report" value="False" />
+            <param name="kit" value="LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424" />
+            <output name="output_splib" file="spectrast2spectrast_irt_output_2_splib.txt" ftype="txt" />
+            <output name="output_pepidx" file="spectrast2spectrast_irt_output_2_pepids.txt" ftype="txt" />
+        </test>
+        -->
+    </tests>
+  <help>
+<![CDATA[
+**What it does**
+
+Filter from spectraST files to swath input files.
+
+
+]]>
+    </help>
+    <citations>
+    </citations>
+</tool>