Mercurial > repos > devteam > sam_to_bam
diff sam_to_bam.xml @ 2:5a5f92086188 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:53:53 -0400 |
| parents | 7095d651c95f |
| children | 4afb4a5f0924 |
line wrap: on
line diff
--- a/sam_to_bam.xml Thu Mar 27 14:04:25 2014 -0400 +++ b/sam_to_bam.xml Tue Oct 13 12:53:53 2015 -0400 @@ -1,97 +1,89 @@ -<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> +<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> - </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> - + </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** -This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. +Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands:: -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml - ------- + samtools sort -O bam -o sorted_input.bam [INPUT SAM] + samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam -**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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ - +]]> </help> + <expand macro="citations"></expand> </tool>