comparison bamtools-filter.xml @ 5:bd735cae4ce6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4

4:3213c223678c

<tool id="bamFilter" name="Filter" version="2.4.0">
    <description>BAM datasets on a variety of attributes</description>
    <requirements>
        <requirement type="package" version="2.4.0">bamtools</requirement>
    </requirements>
    <command>
        <![CDATA[
            cat $script_file > $out_file2;
            #for $bam_count, $input_bam in enumerate( $input_bams ):
                ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
                ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
            #end for
            bamtools
            filter
            -script $script_file
            #for $bam_count, $input_bam in enumerate( $input_bams ):
                -in "localbam_${bam_count}.bam"
            #end for
            -out $out_file1
        ]]>
    </command>
    <configfiles>
        <configfile name="script_file">
            ##Sets up a json configfile for bamtools filter
            ##If there is more than one condition prints brackets and "filters:"
            #if len( $conditions ) > 1
            {
                "filters":
                  [
                  #end if
                  #for $i, $c in enumerate( $conditions, start=1 )
                  { "id": "$i",
                      #for $j, $s in enumerate( $c.filters, start=1 )
                      ##The if below takes care of the comma at the end of last condition within group
                      #if $j != len( $c.filters)
                          "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
                      #else
                          "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
                      #end if
                      #end for
                      ##The if below takes care of the comma at the end of last condition within group
                      #if $i != len( $conditions )
                  },
                  #else
            }
            #end if
            #end for
            #if len( $conditions ) > 1
                #if str( $rule_configuration.rules_selector ) == "True":
                    ],
                    "rule" : "${rule_configuration.rules}"
                #else
                    ]
                #end if
            }
            #end if
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
        <repeat name="conditions" title="Condition" min="1">
            <repeat name="filters" title="Filter" min="1">
                <conditional name="bam_property">
                    <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
                        <option value="alignmentFlag"/>

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="out_file2" />
        <data format="bam" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
            <param name="bam_property_selector" value="mapQuality"/>
            <param name="bam_property_value" value=">20"/>
            <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>
        </test>
    </tests>
    <help>
**What is does**

5:bd735cae4ce6

<tool id="bamFilter" name="Filter" version="2.4.1">
    <description>BAM datasets on a variety of attributes</description>
    <requirements>
        <requirement type="package" version="2.4.0">bamtools</requirement>
    </requirements>
    <command>
        <![CDATA[
            cp '$script_file' '$out_file2' &&
            ln -s '${input_bam}' localbam.bam &&
            ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
            bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1'
        ]]>
    </command>
    <configfiles>
        <configfile name="script_file">
<![CDATA[
<% import json %>
#set $config = dict()
#if $conditions:
    #set $config[ 'filters' ] = []
    #for $i, $condition in enumerate( $conditions, start=1 ):
        #set $filter = dict( id=str( $i ) )
        #for $j, $s in enumerate( $condition.filters, start=1 ):
            #set $filter[ $str( s[ 'bam_property' ][ 'bam_property_selector' ] ) ] = $str( s[ 'bam_property' ][ 'bam_property_value' ] )
        #end for
        $(config[ 'filters' ].append( $filter ))
    #end for
    #if str( $rule_configuration.rules_selector ) == "true":
        #set $config[ 'rule' ] = $rule_configuration.rules
    #end if
#end if
$json.dumps( $config, indent=4 )
]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM dataset(s) to filter" />
        <repeat name="conditions" title="Condition" min="1">
            <repeat name="filters" title="Filter" min="1">
                <conditional name="bam_property">
                    <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
                        <option value="alignmentFlag"/>

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" />
        <data name="out_file1" format="bam" label="${tool.name} on ${on_string}: Filtered BAM" />
    </outputs>
    <tests>
        <test>
            <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
            <param name="bam_property_selector" value="mapQuality"/>
            <param name="bam_property_value" value=">20"/>
            <output name="out_file1" ftype="bam" file="bamtools-test1.bam" />
        </test>
    </tests>
    <help>
**What is does**