<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>