comparison dexseq.xml @ 4:251393b72616 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf

3:f89c9b25feb4

<tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
    <description>Determines differential exon usage from count tables</description>
     <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="0.2.15">r-rjson</requirement>
    </expand>
    <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." />
        <regex match="Error:"
            source="both"
            level="fatal"
            description="Error in the R script." />
    </stdio>

            label="Visualise the analysis results?"
            help="Output an additional HTML file." />
        <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
    </inputs>
    <outputs>
        <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
        <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
            <filter>report is True</filter>
        </data>
    </outputs>
    <tests>
        <!-- Ensure default output works-->

                <param name="factorLevel2" value="control"/>
                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
            </repeat>
            <param name="report" value="False"/>
            <param name="fdr_cutoff" value="1"/>
            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
        </test>
        <!-- Ensure report works-->
        <test expect_num_outputs="2">
            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
            <repeat name="rep_factorName">

                <param name="factorLevel2" value="control"/>
                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
            </repeat>
            <param name="report" value="True"/>
            <param name="fdr_cutoff" value="1"/>
            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
        </test>
        <!-- Ensure two factors works-->
        <test expect_num_outputs="1">
            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
            <repeat name="rep_factorName">

                <param name="factorLevel2" value="pairedend"/>
                <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
            </repeat>
            <param name="report" value="False"/>
            <param name="fdr_cutoff" value="0.05"/>
            <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**Inputs**

DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
factor that affects gene expressions. You also input several secondary factors that might
influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states.
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

SeqType   SingleEnd      PairedEnd
--------- -------------- ---------------
Gender    Female         Male
========= ============== ===============

*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'condition' given in above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.

**Output**

DEXSeq_ generates a tabular file containing the different columns and an optional html report.

4:251393b72616

<tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
    <description>Determines differential exon usage from count tables</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.20.2">r-getopt</requirement>
        <requirement type="package" version="0.2.20">r-rjson</requirement>
    </expand>
    <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." />
        <regex match="Error:"
            source="both"
            level="fatal"
            description="Error in the R script." />
    </stdio>

            label="Visualise the analysis results?"
            help="Output an additional HTML file." />
        <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
    </inputs>
    <outputs>
        <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" />
        <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
            <filter>report is True</filter>
        </data>
    </outputs>
    <tests>
        <!-- Ensure default output works-->

                <param name="factorLevel2" value="control"/>
                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
            </repeat>
            <param name="report" value="False"/>
            <param name="fdr_cutoff" value="1"/>
            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
        </test>
        <!-- Ensure report works-->
        <test expect_num_outputs="2">
            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
            <repeat name="rep_factorName">

                <param name="factorLevel2" value="control"/>
                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
            </repeat>
            <param name="report" value="True"/>
            <param name="fdr_cutoff" value="1"/>
            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
        </test>
        <!-- Ensure two factors works-->
        <test expect_num_outputs="1">
            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
            <repeat name="rep_factorName">

                <param name="factorLevel2" value="pairedend"/>
                <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
            </repeat>
            <param name="report" value="False"/>
            <param name="fdr_cutoff" value="0.05"/>
            <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**Inputs**

DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
DEXSeq_ is capable of handling multiple factors that affect your experiment. The first factor you input is considered to be the primary
factor that affects gene expressions. You can also input several secondary factors that might
influence your experiment but the final output will be changes in genes due to primary factor in the presence of secondary factors. Each factor has two levels/states.
You need to select an 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

SeqType   SingleEnd      PairedEnd
--------- -------------- ---------------
Gender    Female         Male
========= ============== ===============

*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level 2. Here the order of factor levels is important. For example, for the factor 'condition' given in the above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.

**Output**

DEXSeq_ generates a tabular file containing the different columns and an optional html report.