Mercurial > repos > iuc > samtools_bam_to_cram
diff samtools_bam_to_cram.xml @ 1:38fa15df86b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:17:12 -0400 |
| parents | f11c1dd0b4ae |
| children | 205947f54846 |
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--- a/samtools_bam_to_cram.xml Fri May 05 13:12:05 2017 -0400 +++ b/samtools_bam_to_cram.xml Tue May 09 11:17:12 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="1.2.0"> +<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@"> <description>convert BAM alignments to CRAM format</description> <macros> @@ -18,6 +18,13 @@ && #end if + #if $reference_source.reference_source_selector == 'history': + #set ref_fa = 'ref.fa' + ln -s '${reference_source.input_reference}' ref.fa && + #else: + #set ref_fa = str( $reference_source.input_reference.fields.path ) + #end if + samtools view #if $parameter_regions.target_region == "regions_bed_file" -L '${parameter_regions.regions_bed_file}' @@ -25,7 +32,7 @@ -@\${GALAXY_SLOTS:-1} -C - -T '${reference_source.input_reference}' + -T '$ref_fa' -o '${output_alignment}' '${input_alignment}' @@ -43,15 +50,15 @@ <option value="history">History</option> </param> <when value="cached"> - <param name="input_reference" type="select" format="fasta" label="Genome reference FASTA file"> - <options from_data_table="all_fasta"> + <param name="input_reference" type="select" label="Reference genome"> + <options from_data_table="fasta_indexes"> <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" /> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> - <param name="input_reference" type="data" format="fasta" label="Genome reference FASTA file"/> + <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/> </when> </conditional> <conditional name="parameter_regions"> @@ -65,14 +72,14 @@ <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" /> </when> <when value="regions_bed_file"> - <param name="regions_bed_file" type="data" format="bed" - label="only include reads overlapping this BED FILE" argument="-L"/> + <param name="regions_bed_file" argument="-L" type="data" format="bed" + label="Only include reads overlapping this BED file" /> </when> </conditional> </inputs> <outputs> - <data format="cram" name="output_alignment" label="$tool.name on ${on_string}.cram"></data> + <data name="output_alignment" format="cram" label="$tool.name on ${on_string}.cram"></data> </outputs> <tests> @@ -82,7 +89,7 @@ <param name="input_reference" value="test.fa" /> <param name="target_region" value="entire_input_file" /> - <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> <param name="input_alignment" value="test.sam" ftype="sam" /> @@ -90,7 +97,7 @@ <param name="input_reference" value="test.fa" /> <param name="target_region" value="entire_input_file" /> - <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> <param name="input_alignment" value="test.bam" ftype="bam" /> @@ -99,7 +106,7 @@ <param name="target_region" value="region" /> <param name="region_string" value="CHROMOSOME_I" /> - <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> <param name="input_alignment" value="test.bam" ftype="bam" /> @@ -108,18 +115,23 @@ <param name="target_region" value="regions_bed_file" /> <param name="regions_bed_file" value="test.bed" ftype="bed" /> - <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + </test> + <test> + <param name="input_alignment" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" /> + <param name="reference_source_selector" value="cached" /> + <param name="input_reference" value="equCab2chrM" /> + <param name="target_region" value="entire_input_file" /> + <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" /> </test> </tests> - <help> - + <help><![CDATA[ **What this tool does** -Converts alignments from the BAM format to the CRAM format using the SAMTools_ toolkit. The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient. - -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml - </help> +Converts alignments from the BAM format to the CRAM format using the ``samtools view`` command. +The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient. + ]]></help> <expand macro="citations" /> </tool>