comparison multigps.xml @ 50:20687c85887e draft

Uploaded

49:381efb7b880f

<tool id="multigps" name="MultiGPS" version="0.73">
    <description>analyzes collections of multi-condition ChIP-seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

                    #end if
                    --edgerod $rbec.edgerod
                    --diffp $rbec.diffp
                #end if
            #end if
            --out '$output_html.files_path'
            && mv $output_dir/*.html $output_html || true
            && mv $output_dir/*.table.txt $all_events_table || true
            && mv $output_dir/*.counts $replicates_counts || true
        ]]>
    </command>
    <inputs>
        <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
            <validator type="unspecified_build" />

            </when>
            <when value="hide" />
        </conditional>
    </inputs>
    <outputs>
        <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
        <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/>
        <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
            <param name="advanced_options_cond" value="hide" />

50:20687c85887e

<tool id="multigps" name="MultiGPS" version="0.73.0">
    <description>analyzes collections of multi-condition ChIP-seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

                    #end if
                    --edgerod $rbec.edgerod
                    --diffp $rbec.diffp
                #end if
            #end if
            >/dev/null
            --out '$output_html.files_path'
            && cp $output_dir/*.events.txt '$experiment_events' || true
            && mv $output_dir/*.html '$output_html' || true
            && mv $output_dir/*.table.txt '$all_events_table' || true
            && mv $output_dir/*.counts '$replicates_counts' || true
        ]]>
    </command>
    <inputs>
        <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
            <validator type="unspecified_build" />

            </when>
            <when value="hide" />
        </conditional>
    </inputs>
    <outputs>
        <data name="replicates_counts" format="tabular" label="${tool.name} replicates counts on ${on_string}"/>
        <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/>
        <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/>
        <data name="output_html" format="html" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
            <param name="advanced_options_cond" value="hide" />