comparison hd.xml @ 14:883e6381ba29 draft

planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e

13:5b0a95f205ad

<?xml version="1.0" encoding="UTF-8"?>
<tool id="hd" name="Duplex Sequencing Analysis:" version="0.0.14">
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package" version="1.4">matplotlib</requirement>
    </requirements>
    <description>Hamming distance (HD) analysis of tags</description>
    <command>
        python2 $__tool_directory__/hd.py --inputFile "$inputFile" --inputName1 "$inputFile.name" --inputFile2 "$inputFile2" --inputName2 "$inputFile2.name" --sample_size $sampleSize --sep $separator --subset_tag $subsetTag --nproc $nproc $onlyDCS --minFS $minFS --maxFS $maxFS --output_pdf $output_pdf --output_csv $output_csv 
        #if $inputFile2:
        --output_pdf2 $output_pdf2 --output_csv2 $output_csv2
        #end if
    </command>
    <inputs>

        <param name="maxFS" type="integer" label="max family size of the tags" min="0" value="0" help="filters the tags after their family size: Families with larger size are skipped. If max. family size is 0, no upper bound is defined and the maximum family size in the analysis will be the maximum family size of the whole dataset. Default: max. family size = 0."/>
        <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
        <param name="onlyDCS" type="boolean" label="only DCS in the analysis?" truevalue="" falsevalue="--only_DCS" checked="False" help="Only tags, which have a partner tag in the dataset, are included in the analysis."/>
        <param name="subsetTag" type="integer" label="shorten tag in the analysis?" value="0" help="An analysis with shorter tag length, which is specified by this parameter, is simulated. If this parameter is 0 (by default), the tag with its original length is used in the analysis."/>
        <param name="nproc" type="integer" label="number of processors" value="8" help="Number of processor used for computing."/>
    </inputs>
    <outputs>
        <data name="output_csv" format="csv"/>
        <data name="output_csv2" format="csv">
            <filter>inputFile2</filter>

14:883e6381ba29

<?xml version="1.0" encoding="UTF-8"?>
<tool id="hd" name="Duplex Sequencing Analysis: hd" version="0.0.15">
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package" version="1.4">matplotlib</requirement>
    </requirements>
    <description>Hamming distance (HD) analysis of tags</description>
    <command>
        python2 $__tool_directory__/hd.py --inputFile "$inputFile" --inputName1 "$inputFile.name" --inputFile2 "$inputFile2" --inputName2 "$inputFile2.name" --sample_size $sampleSize --sep $separator --subset_tag $subsetTag --nproc $nproc $onlyDCS --minFS $minFS --maxFS $maxFS
		$nr_above_bars --output_pdf $output_pdf --output_csv $output_csv 
        #if $inputFile2:
        --output_pdf2 $output_pdf2 --output_csv2 $output_csv2
        #end if
    </command>
    <inputs>

        <param name="maxFS" type="integer" label="max family size of the tags" min="0" value="0" help="filters the tags after their family size: Families with larger size are skipped. If max. family size is 0, no upper bound is defined and the maximum family size in the analysis will be the maximum family size of the whole dataset. Default: max. family size = 0."/>
        <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
        <param name="onlyDCS" type="boolean" label="only DCS in the analysis?" truevalue="" falsevalue="--only_DCS" checked="False" help="Only tags, which have a partner tag in the dataset, are included in the analysis."/>
        <param name="subsetTag" type="integer" label="shorten tag in the analysis?" value="0" help="An analysis with shorter tag length, which is specified by this parameter, is simulated. If this parameter is 0 (by default), the tag with its original length is used in the analysis."/>
        <param name="nproc" type="integer" label="number of processors" value="8" help="Number of processor used for computing."/>
        <param name="nr_above_bars" type="boolean" label="include numbers above bars?" truevalue="" falsevalue="--nr_above_bars" checked="False" help="The absolute and relative values of the bar can be included or removed in the plot. "/>
 
    </inputs>
    <outputs>
        <data name="output_csv" format="csv"/>
        <data name="output_csv2" format="csv">
            <filter>inputFile2</filter>