# HG changeset patch
# User galaxyp
# Date 1582708590 0
# Node ID 14be5a604bdc86ffbb1db9f7ab8451678efc1aa0

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"

diff -r 000000000000 -r 14be5a604bdc macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Feb 26 09:16:30 2020 +0000
@@ -0,0 +1,23 @@
+<macros>
+    <token name="@VERSION@">2.1.4</token>
+
+    <xml name="requirements">
+    <requirements>
+        <requirement type="package" version="2.1.4">pyprophet</requirement>
+        <yield/>
+    </requirements>
+    </xml>
+
+    <xml name="citations">
+    <citations>
+        <citation type="doi">10.1038/nmeth.4398</citation>
+        <citation type="doi">10.1038/nbt.3908</citation>
+        <citation type="doi">10.1093/bioinformatics/btu686</citation>
+        <citation type="doi">10.1038/nmeth.1584</citation>
+        <yield/>
+    </citations>
+    </xml>
+
+    <token name="@link@">http://openswath.org/en/latest/docs/pyprophet.html</token>
+
+</macros>
diff -r 000000000000 -r 14be5a604bdc pyprophet_subsample.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyprophet_subsample.xml	Wed Feb 26 09:16:30 2020 +0000
@@ -0,0 +1,50 @@
+<tool id="pyprophet_subsample" name="PyProphet subsample" version="@VERSION@.0">
+    <description>
+    Subsample OpenSWATH file
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive">
+    <![CDATA[
+        pyprophet subsample
+        --in='$input'
+        --subsample_ratio=$subsample_ratio
+        $test_mode
+        --out='./output.osw'
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format." />
+        <param argument="--subsample_ratio" type="float" value="1" label="Subsample ratio used per input file (between 0 (0 %) and 1 (100 %))" />
+        <param name="test_mode" type="boolean" truevalue="--test" falsevalue="--no-test" label="Run in test mode with fixed seed" />
+    </inputs>
+    <outputs>
+        <data name="output" format="osw" label="${tool.name} on ${on_string}: subsample.osw" from_work_dir="output.osw" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="merged.osw" ftype="osw" />
+            <param name="subsample_ratio" value="0.5" />
+            <param name="test_mode" value="True" />
+            <output name="output" file="subsample.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
+
+Subsample OpenSWATH file to minimum for integrated scoring.
+
+PyProphet is a Python re-implementation of the mProphet algorithm (Reiter 2010 Nature Methods) optimized for SWATH-MS data acquired by data-independent acquisition (DIA). The algorithm was originally published in (Telemann 2014 Bioinformatics) and has since been extended to support new data types and analysis modes (Rosenberger 2017, Nature biotechnology and Nature methods).
+
+For more information, visit @link@
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
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diff -r 000000000000 -r 14be5a604bdc test-data/output.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular	Wed Feb 26 09:16:30 2020 +0000
@@ -0,0 +1,1 @@
+transition_group_id	decoy	run_id	filename	RT	assay_rt	delta_rt	iRT	assay_iRT	delta_iRT	Sequence	FullPeptideName	Charge	mz	Intensity	aggr_prec_Peak_Area	aggr_prec_Peak_Apex	leftWidth	rightWidth	peak_group_rank	d_score	m_score	id	aggr_Peak_Area	aggr_Peak_Apex	aggr_Fragment_Annotation	ProteinName	m_score_peptide_experiment_wide	m_score_peptide_global	m_score_protein_experiment_wide	m_score_protein_global
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diff -r 000000000000 -r 14be5a604bdc test-data/score_plots.pdf
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diff -r 000000000000 -r 14be5a604bdc test-data/score_report.pdf
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diff -r 000000000000 -r 14be5a604bdc test-data/study_design.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/study_design.tabular	Wed Feb 26 09:16:30 2020 +0000
@@ -0,0 +1,3 @@
+Filename	Condition	BioReplicate	Run
+./TN22.mzML	late	1	1
+./TN23.mzML	early	2	2
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