comparison parse.xml @ 14:bfb00f8fec97 draft

planemo upload for repository https://github.com/open2c/pairtools commit 5997d890c2a3fedff3c66d858cb1629b28138dc0

13:729197476fc1

<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy2" profile="23.2" license="MIT">
    <description>Find ligation pairs in alignments and create pairs.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        pairtools parse
            '$sam_path'
            -c '$chroms_path'
            #if str($assembly_name).strip(): 
                --assembly '$assembly_name'
            #end if
            -o '$output_parsed_pairs'
            --min-mapq '$min_mapq'
            --max-molecule-size '$max_molecule_size'
            $drop_readid
            $drop_seq
            $output_stats

            </when>
            <when value="no"/>
        </conditional>
        <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
            <expand macro="walks_policy_options"/>
        </param>   
        <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
    </inputs>
    <outputs>
        <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
        <data name="parsed_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: parsed.stats">
            <filter>output_stats</filter>
        </data>
    </outputs>
    <tests>

            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
        </test>
        <!--Test 02 with BAM file as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
        </test>
        <!--Test 03 with BAM file as input and minimal mapq of 40-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
        </test>
        <!--Test 04 with BAM file as input and walk policy of 5unique-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
        </test>
        <!--Test 05 with BAM file as input and read id dropped-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_readid" value="true"></param>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
        </test>
        <!--Test 06 with SAM file as input and drop_seq enabled-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_seq" value="true"></param>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
        </test>
        <!--Test 07 with SAM file as input and output_stats enabled-->
        <test expect_num_outputs="2">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>

            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
        </test>
        <!--Test 09 with SAM file as input and add columns-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <conditional name="select_add_columns">
                <param name="add_columns_selection" value="yes"/>
                <param name="add_columns" value="mapq,seq"/>
            </conditional>
            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
        </test>

    </tests>
    <help><![CDATA[
        **Pairtools parse**

        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.

14:bfb00f8fec97

<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
    <description>Find ligation pairs in alignments and create pairs.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #set $output = "output" + str($compress_output)
        ln -s '$output_parsed_pairs' '$output' &&
        pairtools parse
            '$sam_path'
            -c '$chroms_path'
            #if str($assembly_name).strip(): 
                --assembly '$assembly_name'
            #end if
            -o '$output'
            --min-mapq '$min_mapq'
            --max-molecule-size '$max_molecule_size'
            $drop_readid
            $drop_seq
            $output_stats

            </when>
            <when value="no"/>
        </conditional>
        <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
            <expand macro="walks_policy_options"/>
        </param>
        <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output file" />   
        <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
    </inputs>
    <outputs>
        <data name="output_parsed_pairs" format="4dn_pairsam" label="${tool.name} on ${on_string}:  .pairs">
            <change_format>
                <when input="compress_output" value=".gz" format="4dn_pairsam.gz"/>
            </change_format>
        </data>
        <data name="parsed_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: parsed.stats">
            <filter>output_stats</filter>
        </data>
    </outputs>
    <tests>

            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
        </test>
        <!--Test 02 with BAM file as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
        </test>
        <!--Test 03 with BAM file as input and minimal mapq of 40-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
        </test>
        <!--Test 04 with BAM file as input and walk policy of 5unique-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
        </test>
        <!--Test 05 with BAM file as input and read id dropped-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_readid" value="true"></param>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
        </test>
        <!--Test 06 with SAM file as input and drop_seq enabled-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_seq" value="true"></param>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
        </test>
        <!--Test 07 with SAM file as input and output_stats enabled-->
        <test expect_num_outputs="2">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>

            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
        </test>
        <!--Test 09 with SAM file as input and default parameters and assembly name and compressed output--> 
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="compress_output" value="true"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.pairs.gz" decompress="true" lines_diff="10"/>
        </test>
        <!--Test 10 with SAM file as input and add columns-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <conditional name="select_add_columns">
                <param name="add_columns_selection" value="yes"/>
                <param name="add_columns" value="mapq,seq"/>
            </conditional>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
        </test>
    </tests>
    <help><![CDATA[
        **Pairtools parse**

        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.