annotate pepquery2_show_sets.xml @ 0:b9e1e95758e8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597

<tool id="pepquery2_show_sets" name="PepQuery2 Show Sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>PepQueryDB datasets, Parameters, PTMs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
echo "PepQuery2 Show Sets $sets"
#if 'PepQueryDB_datasets' in $sets
  && pepquery -b show_full | sed 's/.*\(NO[.]\)/\1/' | grep '^[N1-9]' | sed 's/[ ][ ]*\$//' | sed 's/[ ][ ]*/\t/g'  > '$pepquerydb'
#end if
#if 'parameter_sets' in $sets
  && pepquery -p show | grep -v INFO | sed 's/^.\[m//' > $parameters
#end if
#if 'printPTM' in $sets
  && pepquery -printPTM | grep -v INFO | sed 's/^.\[m//' > $ptm_list
#end if
    ]]></command>
    <inputs>
        <param name="sets" type="select" multiple="true" optional="false" label="PepQuery Set">
            <option value="PepQueryDB_datasets" selected="true">PepQueryDB Datasets</option>
            <option value="parameter_sets">PepQuery Predefined Parameter Sets</option>
            <option value="printPTM">PepQuery Modifications</option>
        </param>
    </inputs>
    <outputs>
        <data name="pepquerydb" format="tabular" label="PepQueryDB datasets">
           <filter>'PepQueryDB_datasets' in sets</filter>
           <actions>
                <action name="comment_lines" type="metadata" default="1" />
                <action name="column_names" type="metadata" default="NO.,dataset_name,short_name,parameter_set,species,data_type,n_spectra,n_ms_file,data_link" />
            </actions>
        </data>
        <data name="parameters" format="txt" label="PepQuery Predefined Parameter Sets">
           <filter>'parameter_sets' in sets</filter>
        </data>
        <data name="ptm_list" format="tabular" label="PepQuery Modifications">
           <filter>'printPTM' in sets</filter>
           <actions>
                <action name="comment_lines" type="metadata" default="1" />
                <action name="column_names" type="metadata" default="mod_id,mod_name,mod_mass,mod_type,mod_category,unimod_accession" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <output name="pepquerydb">
                <assert_contents>
                    <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**Show available: PepQueryDB Datasets, Parameter Sets, and PTMs** *(Post Translational Modifications)*
    
@PEPQUERY_DOCUMANTATION_URL@

**PepQueryDB Datasets**

    - Shows a table of all the indexed MS/MS datasets available in PepQueryDB.
    - *java -jar pepquery-2.0.2.jar -b show_full*
    - These datasets can be used for the **-b** option in **PepQuery**.
    - The parameter_set value can be used in the **-p** option in **PepQuery**.
    - Columns: NO. dataset_name short_name parameter_set species data_type n_spectra n_ms_file data_link


**PepQuery Predefined Parameter Sets**

    - Shows the predefined Parameter Set Names with the option settings
    - *java -jar pepquery-2.0.2.jar -p show*
    - The parameterset names can be used for the **-p** option in **PepQuery**.


**PepQuery Modifications**

    - Shows a table of the PTMs available
    - *java -jar pepquery-2.0.2.jar -printPTM*
    - The mod_id numbers can be used in the **-fixMOD** and **-varMOD** options in **PepQuery**.
    - Columns: mod_id mod_name mod_mass mod_type mod_category unimod_accession

    ]]></help>
    <expand macro="citations" />
</tool>