comparison picard_ReorderSam.xml @ 5:3d4f1fa26f0e draft

Uploaded

4:ab1f60c26526

<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input="${inputFile}"
      #if $source.indexSource == "built-in"
        --ref="${source.ref.fields.path}"
      #else
        --ref-file="${refFile}"
        --species-name="${source.speciesName}"
        --build-name="${source.buildName}"
        --trunc-names="${source.truncateSeqNames}"
      #end if
      --allow-inc-dict-concord="${allowIncDictConcord}"
      --allow-contig-len-discord="${allowContigLenDiscord}"
      --output-format="${outputFormat}"
      --output="${outFile}"
      --tmpdir "${__new_file_path__}" 
      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
  </command>
  <inputs>
    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
           help="If empty, upload or import a SAM/BAM dataset." />
    <conditional name="source">
      <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
        <option value="built-in">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="built-in">
        <param name="ref" type="select" label="Select a reference genome">
          <options from_data_table="picard_indexes" />
        </param>
      </when>
      <when value="history">
        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
        <param name="speciesName" type="text" value="" label="Species name" />
        <param name="buildName" type="text" value="" label="Build name" />
        <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
      </when>
    </conditional>
    <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
    <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}">
      <change_format>
        <when input="outputFormat" value="sam" format="sam" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <!-- Commands:
      cp test-data/phiX.fasta .
      samtools faidx phiX.fasta
      java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
    -->
      <param name="inputFile" value="picard_RS_input1.bam" />
      <param name="indexSource" value="history" />
      <param name="refFile" value="phiX.fasta" />
      <param name="speciesName" value="phiX174" />
      <param name="buildName" value="" />
      <param name="truncateSeqNames" value="false" />
      <param name="allowIncDictConcord" value="false" />
      <param name="allowContigLenDiscord" value="false" />
      <param name="outputFormat" value="True" />
      <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
    </test>
    <test>
      <!-- Command:
      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input2.sam O=picard_RS_output2.sam REFERENCE=/path/to/phiX/picard_index/phiX.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
      /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
      -->
      <param name="inputFile" value="picard_RS_input2.sam" />
      <param name="indexSource" value="built-in" />
      <param name="ref" value="phiX" />
      <param name="allowIncDictConcord" value="false" />
      <param name="allowContigLenDiscord" value="false" />
      <param name="outputFormat" value="False" />
      <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
    </test>
    <test>
      <!-- Commands:
      cp test-data/picard_RS_input4.fasta .
      samtools faidx picard_RS_input4.fasta
      java -jar CreateSequenceDictionary.jar R=picard_RS_input4.fasta O=picard_RS_input4.dict URI=picard_RS_input4.fasta TRUNCATE_NAMES_AT_WHITESPACE=true SPECIES=phiX174 GENOME_ASSEMBLY=phiX_buildBlah1.1
      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input3.bam O=picard_RS_output3.sam REFERENCE=picard_RS_input4.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false
      picard_RS_input3.bam can be made from picard_RS_input3.sam
      -->
      <param name="inputFile" value="picard_RS_input3.bam" />
      <param name="indexSource" value="history" />
      <param name="refFile" value="picard_RS_input4.fasta" />
      <param name="speciesName" value="phiX174" />
      <param name="buildName" value="phiX_buildBlah1.1" />
      <param name="truncateSeqNames" value="true" />
      <param name="allowIncDictConcord" value="true" />
      <param name="allowContigLenDiscord" value="false" />
      <param name="outputFormat" value="False" />
      <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
    </test>
  </tests>
  <help>

.. class:: infomark

**Purpose**

Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
not the same as sorting as done by the SortSam tool, which sorts by either coordinate
values or query name. The ordering in ReorderSam is based on exact name matching of
contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
not included in the output.

**Picard documentation**

This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.

 .. _Picard-tools: http://www.google.com/search?q=picard+samtools

------

.. class:: infomark 

**Inputs, outputs, and parameters**

For the file that needs to be reordered, either a sam file or a bam file must be supplied.
If a bam file is used, it must be coordinate-sorted. A reference file is also required,
so either a fasta file should be supplied or a built-in reference can be selected.

The output contains the same reads as the input file but the reads have been rearranged so
they appear in the same order as the provided reference file. The tool will output either
bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.

The only extra parameters that can be set are flags for allowing incomplete dict concordance
and allowing contig length discordance. If incomplete dict concordance is allowed, only a
partial overlap of the bam contigs with the new reference sequence contigs is required. By
default it is off, requiring a corresponding contig in the new reference for each read contig.
If contig length discordance is allowed, contig names that are the same between a read and the
new reference contig are allowed even if they have different lengths. This is usually not a
good idea, unless you know exactly what you're doing. It's off by default.

.. class:: warningmark

**Warning on SAM/BAM quality**

Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
to be the only way to deal with SAM/BAM that cannot be parsed.


  </help>
</tool>

5:3d4f1fa26f0e

<tool name="ReorderSam" id="picard_ReorderSam" version="1.126.0">
  <description>reorder reads to match ordering in reference sequences</description>
  <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>
  
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  
  <command>
    @java_options@
    #set $picard_dict = "localref.dict"
    #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
    
    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
       
    #if str( $reference_source.reference_source_selector ) == "history":
        
      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
      QUIET=true
      VERBOSITY=ERROR
      
      &amp;&amp;
      
    #else:
    
      #set $ref_fasta = str( $reference_source.ref_file.fields.path )
    
    #end if
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    ReorderSam
      INPUT="${inputFile}"
      OUTPUT="${outFile}"
      REFERENCE="${ref_fasta}"
      ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
      ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
      
      VALIDATION_STRINGENCY="${validation_stringency}"
      QUIET=true
      VERBOSITY=ERROR
      
  </command>
  
  <inputs>
    
     <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">
        <option value="cached">Local cache</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
          <options from_data_table="picard_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
          <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history"> 
        <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
      </when>
    </conditional>

    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
    <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
    <expand macro="VS" />
    
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
  </outputs>
  <tests>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
      <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
      <param name="allow_incomplete_dict_concordance" value="false"/>
      <param name="allow_contig_length_discordance" value="false"/>
      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

.. class:: infomark

**Purpose**

ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs.  Reads mapped to contigs absent in the new reference are dropped.

@dataset_collections@

----

.. class:: warningmark

Not to be confused with **SortSam**.

@description@

  ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
  S=Boolean                     If true, then allows only a partial overlap of the BAM contigs with the new reference 
                                sequence contigs.  By default, this tool requires a corresponding contig in the new 
                                reference for each read contig  Default value: false. Possible values: {true, false} 
  
  ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
  U=Boolean                     If true, then permits mapping from a read contig to a new reference contig with the same 
                                name but a different length.  Highly dangerous, only use if you know what you are doing.  
                                Default value: false.  Possible values: {true, false} 

@more_info@
  </help>
</tool>