comparison small_rna_maps.xml @ 16:600e2498bd21 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty

15:82fedc576024

<tool id="small_rna_maps" name="small_rna_maps" version="2.6.0">
  <description></description>
  <requirements>
        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>

  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[
          #for $file in $series
              sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name';
              samtools index '$file.inputs.name';
          #end for
          python '$__tool_directory__'/small_rna_maps.py
              --inputs
          #for $file in $series
              '$file.inputs.name'
          #end for
              --sample_names
          #for $sample in $series
              '$sample.inputs.name'
          #end for
          --minsize $minsize
          --maxsize $maxsize
          --cluster $cluster
      #if str($plots_options.plots_options_selector ) == "two_plot":
          --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
          --outputs '$output_tab' '$extra_output_tab';
      #elif str($plots_options.plots_options_selector ) == "global":
          --plot_methods 'Size'
          --outputs '$output_tab';
      #else:
          --plot_methods '${plots_options.first_plot}'
          --outputs '$output_tab' ;
      #end if
      Rscript '$__tool_directory__'/small_rna_maps.r
          --first_dataframe '$output_tab'
          --extra_dataframe '$extra_output_tab'
          --normalization
          #set $norm = ""
          #for $file in $series
                 #set $norm += str($file.normalization)+' '
          #end for
          #set $norm = $norm[:-1]
          '$norm'
          #if $ylimits_cond.ylimits == "no":
              --ymin '' --ymax ''
          #else:
              --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
          #end if
          #if str($plots_options.plots_options_selector ) == "two_plot":
              --first_plot_method '${plots_options.first_plot}'
              --extra_plot_method '${plots_options.extra_plot}'
          #elif str($plots_options.plots_options_selector ) == "global":
              --first_plot_method 'Size'
              --extra_plot_method ''
              --global '${plots_options.mergestrands}'
          #else:
              --first_plot_method '${plots_options.first_plot}'
              --extra_plot_method ''
          #end if
              --output_pdf '$output_pdf'
  ]]></command>
 <inputs>
    <repeat name="series" title="Input" min="1">
        <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"

    </repeat>
    <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
           value="0" help="default value: 0" />
    <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
           value="10000" help="default value: 10000" />
    <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
           value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
    <conditional name="plots_options">
        <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
            <option value="one_plot">Just one plot per chromosome</option>
            <option value="two_plot" selected="True">Two plots per chromosome</option>
            <option value="global">Global read size distributions of aligned reads</option>
        </param>
        <when value="two_plot">
            <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
                <option value="Counts">Counts</option>
                <option value="Coverage">Coverage</option>

            <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
                <option value="nomerge">Do not merge</option>
                <option value="merge">Merge forward and reverse reads</option>
            </param>
        </when>
    </conditional>
    <conditional name="ylimits_cond">
        <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
               help="This limit won't be applied to size distribution plots"/>
        <when value="yes">

    </data>
    <data format="pdf" name="output_pdf" label="small RNA maps" />
</outputs>

    <tests>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_new2.bam" ftype="bam" />
                <param name="normalization" value="2.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
            <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="ylimits" value="yes" />
            <param name="ymin" value="-5" />
            <param name="ymax" value="5" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
            <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="5" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Coverage" />
            <output file="input1_coverage_cluster5.tab" name="output_tab" />
            <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="20" />
            <param name="maxsize" value="30" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Size" />
            <output file="input1_min20_max30_size.tab" name="output_tab" />
            <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Mean" />
            <output file="input1_mean.tab" name="output_tab" />
            <output file="input1__single_plot_mean.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Median" />
            <output file="input1_median.tab" name="output_tab" />
            <output file="input1_single_plot_median.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="2.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
            <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="ylimits" value="yes" />
            <param name="ymin" value="-5" />
            <param name="ymax" value="5" />
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Size" />
            <output file="input1_input2_counts.tab" name="output_tab" />
            <output file="input1_input2_size.tab" name="extra_output_tab" />
            <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Coverage" />
            <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
            <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="global" />
            <param name="mergestrands" value="nomerge" />
            <param name="first_plot" value="Size" />
            <output file="size.tab" name="output_tab" />
            <output file="global_nomerge.pdf" name="output_pdf" />
        </test>
        <test>
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="cluster" value="0" />
            <param name="plots_options_selector" value="global" />
            <param name="mergestrands" value="merge" />
            <param name="first_plot" value="Size" />
            <output file="size.tab" name="output_tab" />
            <output file="global_merge.pdf" name="output_pdf" />

16:600e2498bd21

<tool id="small_rna_maps" name="small_rna_maps" version="2.7.0">
  <description></description>
  <requirements>
        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>

  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[
          #for $file in $series
              sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name' &&
              samtools index '$file.inputs.name' &&
          #end for
          python '$__tool_directory__'/small_rna_maps.py
              --inputs
              #for $file in $series
                  '$file.inputs.name'
              #end for
                  --sample_names
              #for $sample in $series
                  '$sample.inputs.name'
              #end for
              --minsize $minsize
              --maxsize $maxsize
              #if str($plots_options.plots_options_selector ) == "two_plot":
                  --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
                  --outputs '$output_tab' '$extra_output_tab' &&
              #elif str($plots_options.plots_options_selector ) == "global":
                  --plot_methods 'Size'
                  --outputs '$output_tab' &&
              #elif str($plots_options.plots_options_selector ) == "cluster":
                  --plot_methods 'Counts'
                  --outputs '$output_tab'
                  --cluster ${plots_options.cluster} &&
              #else:
                  --plot_methods '${plots_options.first_plot}'
                  --outputs '$output_tab' &&
              #end if

          Rscript '$__tool_directory__'/small_rna_maps.r
              --first_dataframe '$output_tab'
              --extra_dataframe '$extra_output_tab'
              --normalization
              #set $norm = ""
              #for $file in $series
                     #set $norm += str($file.normalization)+' '
              #end for
              #set $norm = $norm[:-1]
              '$norm'
              #if $ylimits_cond.ylimits == "no":
                  --ymin '' --ymax ''
              #else:
                  --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
              #end if
              #if str($plots_options.plots_options_selector ) == "two_plot":
                  --first_plot_method '${plots_options.first_plot}'
                  --extra_plot_method '${plots_options.extra_plot}'
              #elif str($plots_options.plots_options_selector ) == "global":
                  --first_plot_method 'Size'
                  --extra_plot_method ''
                  --global '${plots_options.mergestrands}'
              #else:
                  --first_plot_method '${plots_options.first_plot}'
                  --extra_plot_method ''
              #end if
              --output_pdf '$output_pdf'
  ]]></command>
 <inputs>
    <repeat name="series" title="Input" min="1">
        <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"

    </repeat>
    <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
           value="0" help="default value: 0" />
    <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
           value="10000" help="default value: 10000" />
    <conditional name="plots_options">
        <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
            <option value="one_plot">Just one plot per chromosome</option>
            <option value="two_plot" selected="True">Two plots per chromosome</option>
            <option value="global">Global read size distributions of aligned reads</option>
            <option value="cluster">Map read clusters</option>
        </param>
        <when value="two_plot">
            <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
                <option value="Counts">Counts</option>
                <option value="Coverage">Coverage</option>

            <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
                <option value="nomerge">Do not merge</option>
                <option value="merge">Merge forward and reverse reads</option>
            </param>
        </when>
        <when value="cluster">
            <param name="first_plot" type="hidden" value="Counts"/>
            <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
                   help="Sets the distance (in nt) below which reads are clustered to a single median position" />
        </when>
    </conditional>
    <conditional name="ylimits_cond">
        <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
               help="This limit won't be applied to size distribution plots"/>
        <when value="yes">

    </data>
    <data format="pdf" name="output_pdf" label="small RNA maps" />
</outputs>

    <tests>
        <test> <!-- 1 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_new2.bam" ftype="bam" />
                <param name="normalization" value="2.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
            <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
        </test>
        <test> <!-- 2 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="ylimits" value="yes" />
            <param name="ymin" value="-5" />
            <param name="ymax" value="5" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
            <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
        </test>
        <test> <!-- 3 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="cluster" />
            <param name="first_plot" value="Counts" />
            <param name="cluster" value="5" />
            <output file="clustering.tab" name="output_tab" />
            <output file="clustering.pdf" name="output_pdf" />
        </test>
        <test> <!-- 4 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="20" />
            <param name="maxsize" value="30" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Size" />
            <output file="input1_min20_max30_size.tab" name="output_tab" />
            <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
        </test>
        <test> <!-- 5 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Mean" />
            <output file="input1_mean.tab" name="output_tab" />
            <output file="input1__single_plot_mean.pdf" name="output_pdf" />
        </test>
        <test> <!-- 6 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Median" />
            <output file="input1_median.tab" name="output_tab" />
            <output file="input1_single_plot_median.pdf" name="output_pdf" />
        </test>
        <test> <!-- 7 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="2.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
            <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
        </test>
        <test> <!-- 8 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="ylimits" value="yes" />
            <param name="ymin" value="-5" />
            <param name="ymax" value="5" />
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Size" />
            <output file="input1_input2_counts.tab" name="output_tab" />
            <output file="input1_input2_size.tab" name="extra_output_tab" />
            <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
        </test>
        <test> <!-- 9 -->
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Coverage" />
            <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
            <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
        </test>
        <test> <!-- 10 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="global" />
            <param name="mergestrands" value="nomerge" />
            <param name="first_plot" value="Size" />
            <output file="size.tab" name="output_tab" />
            <output file="global_nomerge.pdf" name="output_pdf" />
        </test>
        <test> <!-- 11 -->
            <repeat name="series">
                <param name="inputs" value="input1.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <repeat name="series">
                <param name="inputs" value="input2.bam" ftype="bam" />
                <param name="normalization" value="1.0" />
            </repeat>
            <param name="minsize" value="0" />
            <param name="maxsize" value="10000" />
            <param name="plots_options_selector" value="global" />
            <param name="mergestrands" value="merge" />
            <param name="first_plot" value="Size" />
            <output file="size.tab" name="output_tab" />
            <output file="global_merge.pdf" name="output_pdf" />