comparison sam_to_bam.xml @ 2:5a5f92086188 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

1:7095d651c95f

<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3">
  <description>converts SAM format to BAM format</description>
  <requirements>
    <requirement type="package" version="0.1.19">samtools</requirement>
  </requirements>
  <command interpreter="python">
    sam_to_bam.py
      --input1=$source.input1
      #if $source.index_source == "history":
        --dbkey=${ref_file.metadata.dbkey} 
        --ref_file=$source.ref_file
      #else
        --dbkey=${input1.metadata.dbkey} 
      #end if
      --output1=$output1
      --index_dir=${GALAXY_DATA_INDEX_DIR}
  </command>
  <inputs>
    <conditional name="source">
      <param name="index_source" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
        </param>
      </when>
      <when value="history">
        <param name="input1" type="data" format="sam" label="Convert SAM file" />
        <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
      <actions>
        <conditional name="source.index_source">
          <when value="cached">
            <action type="metadata" name="dbkey">
              <option type="from_param" name="source.input1" param_attribute="dbkey" />
            </action>
          </when>
          <when value="history">
            <action type="metadata" name="dbkey">
              <option type="from_param" name="source.ref_file" param_attribute="dbkey" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
  </outputs>
  <tests>
    <test>
      <!--
      Sam-to-Bam command:
      cp test-data/chr_m.fasta .
      samtools faidx chr_m.fasta
      samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
      samtools sort unsorted.bam sam_to_bam_out1
      chr_m.fasta is the reference file (chrM from equCab2)
      -->
      <param name="index_source" value="history" /> 
      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
      <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
      <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
    </test>
    <test>
      <!--
      Sam-to-Bam command:
      samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
      samtools sort unsorted.bam sam_to_bam_out2
      chr_m.fasta is the reference file and the index chr_m.fasta.fai 
      these should be in the same directory, and chrM is from equCab2
      -->
      <param name="index_source" value="cached" />
      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
      <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
    </test>
  </tests>
  <help>

**What it does**

This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.

.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml

------

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_

  </help>
</tool>

2:5a5f92086188

<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
  <description>convert SAM to BAM</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio"></expand>
  <expand macro="version_command"></expand>
  <command>
    <![CDATA[
        #if $source.index_source == "history":
          ln -s $source.ref_file input.fa &&
          samtools faidx input.fa &&
        #else
          ln -s ${source.index.fields.path} input.fa &&
          ln -s ${source.index.fields.path}.fai input.fa.fai &&
        #end if
        samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
    ]]>
    </command>
    <inputs>
        <conditional name="source">
            <param label="Choose the source for the reference genome" name="index_source" type="select">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">
                <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data">
                    <validator type="unspecified_build" />
                    <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
                </param>
                <param label="Using reference genome" name="index" type="select">
                    <options from_data_table="fasta_indexes">
                        <filter column="1" key="dbkey" ref="input1" type="data_meta" />
                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param format="sam" label="SAM file to convert" name="input1" type="data" />
                <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1">
            <actions>
                <conditional name="source.index_source">
                    <when value="cached">
                        <action name="dbkey" type="metadata">
                            <option name="source.input1" param_attribute="dbkey" type="from_param" />
                        </action>
                    </when>
                    <when value="history">
                        <action name="dbkey" type="metadata">
                            <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="index_source" value="history" />
            <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
            <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
        </test>
        <test>
            <param name="index_source" value="history" />
            <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
            <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands::

  samtools sort -O bam -o sorted_input.bam [INPUT SAM] 
  samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam

]]>
  </help>
  <expand macro="citations"></expand>
</tool>