comparison samtools_view.xml @ 14:5826298f6a73 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e

13:0dbf49c414ae

<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
    <macros>
        <import>macros.xml</import>
        <token name="@REF_DATA@">
            ## additional reference data

                    #if $input.is_of_type('sam') or $std_filters or $reg_filters:
                        ## There is no index or we cannot use it because we are
                        ## not dealing with all of the reads in the indexed
                        ## file. We have to do an extra pass over the input to
                        ## count the reads to subsample.
                        sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` &&
                    #else:
                        ## We can get the count of reads to subsample using
                        ## an inexpensive call to idxstats.
                        sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` &&
                    #end if
                #end if
            #end if

            ## call samtools view

                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 21) sampling options-->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                    <conditional name="output_format">
                        <param name="oformat" value="input" />
                    </conditional>
                </conditional>
            </conditional>
            <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="6" />
        </test>
        <!-- 22) -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                    <conditional name="output_format">
                        <param name="oformat" value="input" />
                    </conditional>
                </conditional>
            </conditional>
            <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="6" />
        </test>
        <!-- 26) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">

14:5826298f6a73

<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
    <macros>
        <import>macros.xml</import>
        <token name="@REF_DATA@">
            ## additional reference data

                    #if $input.is_of_type('sam') or $std_filters or $reg_filters:
                        ## There is no index or we cannot use it because we are
                        ## not dealing with all of the reads in the indexed
                        ## file. We have to do an extra pass over the input to
                        ## count the reads to subsample.
                        sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
                    #else:
                        ## We can get the count of reads to subsample using
                        ## an inexpensive call to idxstats.
                        sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
                    #end if
                #end if
            #end if

            ## call samtools view

                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 21) sampling options target < total reads -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                    <conditional name="output_format">
                        <param name="oformat" value="input" />
                    </conditional>
                </conditional>
            </conditional>
            <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />
        </test>
        <!-- 22) target > total reads -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                    <conditional name="output_format">
                        <param name="oformat" value="input" />
                    </conditional>
                </conditional>
            </conditional>
            <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />
        </test>
        <!-- 26) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">