comparison velvetg.xml @ 2:8d09f8be269e draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"

1:5da9a0e2fb2d

<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.1">
  <description>Velvet sequence assembler for very short reads</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command><![CDATA[
    velvetg 2>&1 | grep "Version" | sed -e 's/Version //'
  ]]></version_command>
  <command><![CDATA[
ln -s '$input.extra_files_path'/Roadmaps &&
ln -s '$input.extra_files_path'/Sequences &&
velvetg .
#if $generate_amos.afg  == "yes":
    -amos_file $generate_amos.afg
#end if
#if $unused_reads.generate_unused  == "yes":
    -unused_reads $unused_reads.generate_unused
#end if
$read_trkg
#if $coverage.cutoff == "auto":
    -cov_cutoff auto
#elif $coverage.cutoff == "value":
    -cov_cutoff $coverage.cov_cutoff
#end if
#if $expected.coverage == "auto":
    -exp_cov auto
#elif $expected.coverage == "value":
    -exp_cov $expected.exp_cov
#end if
#if $contig_lgth.use_contig_lgth == "yes":
    -min_contig_lgth $contig_lgth.min_contig_lgth
#end if
#if $reads.paired == "yes":
    #if int($reads.ins_length) > 0:
        -ins_length $reads.ins_length
    #end if
    #if $reads.options.advanced == "yes":
        #if int($reads.options.ins_length_sd) > 0:
            -ins_length_sd $reads.options.ins_length_sd
        #end if
        #if int($reads.options.ins_length2) > 0:
            -ins_length2 $reads.options.ins_length2
        #end if
        #if int($reads.options.ins_length2_sd) > 0:
            -ins_length2_sd $reads.options.ins_length2_sd
        #end if
        #if int($reads.options.ins_length_long) > 0:
            -ins_length_long $reads.options.ins_length_long
        #end if
        #if int($reads.options.ins_length_long_sd) > 0:
            -ins_length_long_sd $reads.options.ins_length_long_sd
        #end if
        #if int($reads.options.max_branch_length) > 0:
            -max_branch_length $reads.options.max_branch_length
        #end if
        #if int($reads.options.max_divergence) > 0:
            -max_divergence $reads.options.max_divergence
        #end if
        #if int($reads.options.max_gap_count) > 0:
            -max_gap_count $reads.options.max_gap_count
        #end if
        #if int($reads.options.min_pair_count) > 0:
            -min_pair_count $reads.options.min_pair_count
        #end if
        #if int($reads.options.max_coverage) > 0:
            -max_coverage $reads.options.max_coverage
        #end if
        #if int($reads.options.long_mult_cutoff) > 0:
            -long_mult_cutoff $reads.options.long_mult_cutoff
        #end if
        $reads.options.scaffolding
    #end if
#end if
  ]]></command>
  <inputs>
    <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
    <conditional name="generate_amos">
      <param name="afg" type="select" label="Generate a AMOS.afg file">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no"/>
      <when value="yes"/>
    </conditional>

    <conditional name="unused_reads">
      <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no"/>
      <when value="yes"/>
    </conditional>

    <conditional name="last_graph">
      <param name="generate_graph" type="select" label="Generate velvet LastGraph file">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no"/>
      <when value="yes"/>
    </conditional>

    <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />

    <conditional name="coverage">
      <param name="cutoff" type="select" label="Coverage cutoff" help="">
        <option value="none">None</option>
        <option value="auto">Automatically Determined</option>
        <option value="value">Specify Cutoff Value</option>

      <when value="auto"/>
      <when value="value">
        <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" />
      </when>
    </conditional>

    <conditional name="expected">
      <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
        <option value="none">None</option>
        <option value="auto">Automatically Determined</option>
        <option value="value">Specify Expected Value</option>

      <when value="value">
        <param name="exp_cov" value="10.0" label="Remove nodes with coverage below" type="float" />
      </when>
    </conditional>

    <conditional name="contig_lgth">
      <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no"/>
      <when value="yes">
        <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
      </when>
    </conditional>

    <conditional name="reads">
      <param name="paired" type="select" label="Using Paired Reads">
        <option value="no">No</option>
        <option value="yes">Yes</option>

          <when value="no"/>
          <when value="yes">
            <param name="ins_length_sd" value="-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="ins_length2" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
            <param name="ins_length2_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="ins_length_long" value="-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/>
            <param name="ins_length_long_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="max_branch_length" value="-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/>
            <param name="max_divergence" value="-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/>
            <param name="max_gap_count" value="-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/>
            <param name="min_pair_count" value="-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/>
            <param name="max_coverage" value="-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/>
            <param name="long_mult_cutoff" value="-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/>
            <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/>

          </when>
        </conditional>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2">
      <filter>read_trkg is True</filter>
    </data>
    <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
      <filter>last_graph['generate_graph'] == "yes"</filter>
    </data>
    <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
      <filter>generate_amos['afg'] == "yes"</filter>
    </data>
    <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
      <filter>unused_reads['generate_unused'] == "yes"</filter>
    </data>
    <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
    <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="velveth_test1/output.html" ftype="velvet">
        <composite_data value="velveth_test1/Sequences" />
        <composite_data value="velveth_test1/Roadmaps" />
        <composite_data value="velveth_test1/Log"/>
      </param>
      <param name="afg" value="yes" />
      <param name="generate_unused" value="yes" />
      <param name="generate_graph" value="no" />
      <param name="read_trkg" value="-read_trkg no" />
      <param name="cutoff" value="auto" />
      <param name="coverage" value="auto" />
      <param name="use_contig_lgth" value="no" />
      <param name="paired" value="no" />
      <!--
      <output name="LastGraph" file="velvetg_test1/lastgraph.txt"/>
      -->
      <output name="velvet_asm" file="velvetg_test1/amos.afg" />
      <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" />
      <output name="stats" file="velvetg_test1/stats.csv" />
      <output name="contigs" file="velvetg_test1/contigs.fa" />
    </test>
  </tests>
  <help><![CDATA[
**What it does**

2:8d09f8be269e

<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.2">
  <description>Velvet sequence assembler for very short reads</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command><![CDATA[
    velvetg 2>&1 | grep "Version" | sed -e 's/Version //'
  ]]></version_command>
  <command><![CDATA[
    ln -s '$input.extra_files_path'/Roadmaps &&
    ln -s '$input.extra_files_path'/Sequences &&
    velvetg .
           #if 'amos' in $add_out:
               -amos_file yes
           #end if
           #if 'unused' in $add_out:
               -unused_reads yes
           #end if
           $read_trkg
           #if $coverage.cutoff == "auto":
               -cov_cutoff auto
           #elif $coverage.cutoff == "value":
               -cov_cutoff $coverage.cov_cutoff
           #end if
           #if $expected.coverage == "auto":
               -exp_cov auto
           #elif $expected.coverage == "value":
               -exp_cov $expected.exp_cov
           #end if
           #if $contig_lgth.use_contig_lgth == "yes":
               -min_contig_lgth $contig_lgth.min_contig_lgth
           #end if
           #if $reads.paired == "yes":
               #if int($reads.ins_length) > 0:
                   -ins_length $reads.ins_length
               #end if
               #if $reads.options.advanced == "yes":
                   #if int($reads.options.ins_length_sd) > 0:
                       -ins_length_sd $reads.options.ins_length_sd
                   #end if
                   #if int($reads.options.ins_length2) > 0:
                       -ins_length2 $reads.options.ins_length2
                   #end if
                   #if int($reads.options.ins_length2_sd) > 0:
                       -ins_length2_sd $reads.options.ins_length2_sd
                   #end if
                   #if int($reads.options.ins_length3) > 0:
                       -ins_length3 $reads.options.ins_length3
                   #end if
                   #if int($reads.options.ins_length3_sd) > 0:
                       -ins_length3_sd $reads.options.ins_length3_sd
                   #end if
                   #if int($reads.options.ins_length4) > 0:
                       -ins_length4 $reads.options.ins_length4
                   #end if
                   #if int($reads.options.ins_length4_sd) > 0:
                       -ins_length4_sd $reads.options.ins_length4_sd
                   #end if
                   #if int($reads.options.ins_length_long) > 0:
                       -ins_length_long $reads.options.ins_length_long
                   #end if
                   #if int($reads.options.ins_length_long_sd) > 0:
                       -ins_length_long_sd $reads.options.ins_length_long_sd
                   #end if
                   #if int($reads.options.max_branch_length) > 0:
                       -max_branch_length $reads.options.max_branch_length
                   #end if
                   #if int($reads.options.max_divergence) > 0:
                       -max_divergence $reads.options.max_divergence
                   #end if
                   #if int($reads.options.max_gap_count) > 0:
                       -max_gap_count $reads.options.max_gap_count
                   #end if
                   #if int($reads.options.min_pair_count) > 0:
                       -min_pair_count $reads.options.min_pair_count
                   #end if
                   #if int($reads.options.max_coverage) > 0:
                       -max_coverage $reads.options.max_coverage
                   #end if
                   #if int($reads.options.long_mult_cutoff) > 0:
                       -long_mult_cutoff $reads.options.long_mult_cutoff
                   #end if
                   $reads.options.scaffolding
               #end if
           #end if
  ]]></command>
  <inputs>
    <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
    <conditional name="coverage">
      <param name="cutoff" type="select" label="Coverage cutoff" help="">
        <option value="none">None</option>
        <option value="auto">Automatically Determined</option>
        <option value="value">Specify Cutoff Value</option>

      <when value="auto"/>
      <when value="value">
        <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" />
      </when>
    </conditional>
    <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />
    <conditional name="contig_lgth">
      <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no"/>
      <when value="yes">
        <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
      </when>
    </conditional>
    <conditional name="expected">
      <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
        <option value="none">None</option>
        <option value="auto">Automatically Determined</option>
        <option value="value">Specify Expected Value</option>

      <when value="value">
        <param name="exp_cov" value="10.0" label="Remove nodes with coverage below" type="float" />
      </when>
    </conditional>

    <param name="add_out" type="select" multiple="true" optional="true" label="Additional outputs" help="">
        <option value="amos">Generate a AMOS.afg file</option>
        <option value="unused">Generate a UnusedReads fasta file</option>
        <option value="lastgraph">Generate velvet LastGraph file</option>
    </param>

    <conditional name="reads">
      <param name="paired" type="select" label="Using Paired Reads">
        <option value="no">No</option>
        <option value="yes">Yes</option>

          <when value="no"/>
          <when value="yes">
            <param name="ins_length_sd" value="-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="ins_length2" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
            <param name="ins_length2_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="ins_length3" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
            <param name="ins_length3_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="ins_length4" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
            <param name="ins_length4_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="ins_length_long" value="-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/>
            <param name="ins_length_long_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/>
            <param name="max_branch_length" value="-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/>
            <param name="max_divergence" value="-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/>
            <param name="max_gap_count" value="-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/>
            <param name="min_pair_count" value="-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/>
            <param name="max_coverage" value="-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/>
            <param name="long_mult_cutoff" value="-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/>
            <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/>
          </when>
        </conditional>
      </when>
    </conditional>
<!-- TODO
-coverage_mask
-paired_exp_fraction
-alignments
-exportFiltered
-clean
-very_clean
-shortMatePaired-->
  </inputs>
  <outputs>
    <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2">
      <filter>read_trkg is True</filter>
    </data>
    <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
      <filter>'lastgraph' in add_out</filter>
    </data>
    <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
      <filter>'amos' in add_out</filter>
    </data>
    <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
      <filter>'unused' in add_out</filter>
    </data>
    <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
    <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
  </outputs>
  <tests>
    <test expect_num_outputs="5">
      <param name="input" value="velvetg_paired.out" ftype="velvet" >
        <composite_data value='velvetg_paired/Sequences'/>
        <composite_data value='velvetg_paired/Roadmaps'/>
        <composite_data value='velvetg_paired/Log'/>
      </param>
      <param name="add_out" value="amos,unused,lastgraph" />
      <param name="read_trkg" value="-read_trkg no" />
      <param name="cutoff" value="auto" />
      <param name="coverage" value="auto" />
      <param name="use_contig_lgth" value="no" />
      <param name="paired" value="no" />
      <output name="velvet_asm" file="velvetg_paired/velvet_asm.afg" compare="diff"/>
      <output name="unused_reads_fasta" file="velvetg_paired/UnusedReads.fa" compare="diff"/>
      <output name="LastGraph" file="velvetg_paired/lastgraph.txt" compare="diff"/>
      <output name="stats" file="velvetg_paired/stats.txt" compare="diff"/>
      <output name="contigs" file="velvetg_paired/contigs.fa" compare="diff"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**