comparison dexseq.xml @ 1:f1c406f9554c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232

0:4ca0e679f21e

<tool id="dexseq" name="DEXSeq" version="1.0">
    <description>Determines differential exon usage from count tables</description>
    <requirements>
        <requirement type="package" version="1.14">dexseq</requirement>
    </requirements>
    <code file="dexseq_helper.py" />
    <stdio>
        <regex match="Execution halted" 
           source="both" 
           level="fatal" 
           description="Execution halted." />
        <regex match="Input-Error 01" 
           source="both" 
           level="fatal" 
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occured, please check your input carefully and contact your administrator." />

    </version_command>
    <command>
    <![CDATA[
        mkdir ./html_out &&
        #import json
        Rscript $__tool_directory__/dexseq.R
            -o "$dexseq_out"
            -p \${GALAXY_SLOTS:-4}
            #set $temp_factor_names = list()
            #for $factor in $rep_factorName:
                #set $temp_factor = list()
                #set $count_files1 = list()

            -c $fdr_cutoff

            #if $report:
                -r ./html_out
                &&
                mkdir $htmlreport.extra_files_path
                &&
                cp ./html_out/testForDEU.html $htmlreport
                &&
                cp -r ./html_out/* $htmlreport.extra_files_path
            #end if

    ]]>
    </command>
    <inputs>
        <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
        <repeat name="rep_factorName" title="Factor" min="1">
            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
                help="Only letters, numbers and underscores will be retained in this field">
                <sanitizer>
                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
                </sanitizer>
            </param>

    </tests>
    <help>
    <![CDATA[
.. class:: infomark

**What it does** 

Inference of differential exon usage in RNA-Seq.


**Inputs**

You need to select appropriate count table from your history for each factor level.

The following table gives some examples of factors and their levels:

========= ============== ===============
Factor    Factor level 1 Factor level 2 
--------- -------------- ---------------
condition Knockdown      Wildtype
--------- -------------- ---------------
treatment Treated        Untreated
--------- -------------- ---------------

1:f1c406f9554c

<tool id="dexseq" name="DEXSeq" version="1.20.1">
    <description>Determines differential exon usage from count tables</description>
    <requirements>
        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="0.2.15">r-rjson</requirement>
    </requirements>
    <code file="dexseq_helper.py" />
    <stdio>
        <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted." />
        <regex match="Input-Error 01"
           source="both"
           level="fatal"
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occured, please check your input carefully and contact your administrator." />

    </version_command>
    <command>
    <![CDATA[
        mkdir ./html_out &&
        #import json
        Rscript '$__tool_directory__/dexseq.R'
            -o '$dexseq_out'
            -p \${GALAXY_SLOTS:-4}
            #set $temp_factor_names = list()
            #for $factor in $rep_factorName:
                #set $temp_factor = list()
                #set $count_files1 = list()

            -c $fdr_cutoff

            #if $report:
                -r ./html_out
                &&
                mkdir '$htmlreport.extra_files_path'
                &&
                cp ./html_out/testForDEU.html $htmlreport
                &&
                cp -r ./html_out/* '$htmlreport.extra_files_path'
            #end if

    ]]>
    </command>
    <inputs>
        <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
        <repeat name="rep_factorName" title="Factor" min="1">
            <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
                help="Only letters, numbers and underscores will be retained in this field">
                <sanitizer>
                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
                </sanitizer>
            </param>

    </tests>
    <help>
    <![CDATA[
.. class:: infomark

**What it does**

Inference of differential exon usage in RNA-Seq.


**Inputs**

You need to select appropriate count table from your history for each factor level.

The following table gives some examples of factors and their levels:

========= ============== ===============
Factor    Factor level 1 Factor level 2
--------- -------------- ---------------
condition Knockdown      Wildtype
--------- -------------- ---------------
treatment Treated        Untreated
--------- -------------- ---------------