--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diapysef.xml	Fri Mar 06 07:16:26 2020 -0500
@@ -0,0 +1,111 @@
+<tool id="diapysef" name="diapysef library generation" version="0.3.5.0">
+    <description>generates spectral library for DIA analysis</description>
+    <requirements>
+        <requirement type="package" version="0.3.5">diapysef</requirement>
+        <requirement type="package" version="1.0.1">pandas</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+        python '${diapysef_script}'
+
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="diapysef_script"><![CDATA[
+
+import diapysef as dp
+import pandas as pd
+
+msms = pd.read_csv("$input_msms", sep="\t")
+evidence = pd.read_csv("$input_evidence", sep="\t")
+irt = pd.read_csv("$input_irtassays", sep="\t")
+ptsv = dp.pasef_to_tsv(evidence, msms, irt_file=irt, ion_mobility=None, rt_alignment="$alignment")
+ptsv.to_csv("$output_tabular", sep="\t", index=False)
+
+
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="input_msms" type="data" format="tabular" label="MaxQuant output file msms.txt" help="" />
+        <param name="input_evidence" type="data" format="tabular" label="MaxQuant output file evidence.txt" help="" />
+        <param name="input_irtassays" type="data" format="tabular" label="Retention time alignment peptides" help="tabular file containing peptides for the alignment, e.g. iRTs or ciRTs" />
+        <param name="alignment" type="select" display="radio" label="RT alignment method" help="" >
+            <option value="linear" selected="True">linear</option>
+            <option value="nonlinear">lowess</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: spectral library" from_work_dir="mqout.tabular" />
+        <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: RT calibration curves" from_work_dir="rtcalibration.pdf" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_msms" value="msms_cut.tabular" ftype="tabular" />
+            <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" />
+            <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" />
+            <param name="alignment" value="linear" />
+            <output name="output_pdf" file="rtcalibration1.pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_msms" value="msms_cut.tabular" ftype="tabular" />
+            <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" />
+            <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" />
+            <param name="alignment" value="nonlinear" />
+            <output name="output_pdf" file="rtcalibration2.pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_msms" value="msms_cut.tabular" ftype="tabular" />
+            <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" />
+            <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" />
+            <param name="alignment" value="nonlinear" />
+            <output name="output_tabular" >
+            <assert_contents>
+                <has_text text="transition_group_id" />
+                <has_text text="LibraryIntensity" />
+                <has_text text="(Acetylation)DGLDAASYYAPVR" />
+                <has_text text="sp|Biognosys_pep-h|iRT-Kit_WR_fusion" />
+                <has_text text="sp|Biognosys_pep-k|iRT-Kit_WR_fusion" />
+                <has_n_columns n="11" />
+            </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+
+Diapysef enables generating a DIA library. For more information: http://openswath.org/en/latest/docs/librarygeneration.html
+
+For most data-independent acquisition (DIA) analysis, a well-represented spectral library is required for precursors, peptide, and protein identifications. Currently, we support library generation with the diapysef package directly from a MaxQuant analysis of several DDA runs. 
+
+**Inputs**
+
+    - msms.txt and evidence.txt (output files from MaxQuant)
+    - peptides used for retention time alignment e.g. iRTs or ciRTs
+
+        - Tabular file with at least three columns for precursor charge, normalized retention time and modified peptide sequence
+        - The headers of the columns must be named "PrecursorCharge" "NormalizedRetentionTime" "ModifiedPeptideSequence"
+
+
+            ::
+
+              PrecursorCharge     NormalizedRetentionTime    ModifiedPeptideSequence
+                     2                       53.2                 ADVTPADFSEWSK
+                     3                       52.9                 ADVTPADFSEWSK
+                     2                       43.6                 DGLDAASYYAPVR
+                    ...
+                    ...
+
+
+**Potential next Steps**
+
+After generating the spectral library with diapysef, the tabular file can be imported into OpenSwathAssayGenerator and OpenSwathDecoyGenerator to refine the library.
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nbt.2841</citation>
+    </citations>
+</tool>