Mercurial > repos > iuc > samtools_cram_to_bam
diff samtools_cram_to_bam.xml @ 4:1551b0dd2d16 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:11:03 +0000 |
| parents | 858ada516d8f |
| children | 634df184b2a8 |
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--- a/samtools_cram_to_bam.xml Sat Jul 31 07:26:19 2021 +0000 +++ b/samtools_cram_to_bam.xml Tue Sep 28 16:11:03 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy1"> +<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>convert CRAM alignments to BAM format</description> <macros> @@ -9,52 +9,31 @@ <expand macro="version_command"/> <command><![CDATA[ - #set input_cram = "input.cram" - ln -s '${input_alignment}' '${input_cram}' && - #if str( $input_alignment.metadata.cram_index ) != "None": - ln -f -s '${input_alignment.metadata.cram_index}' '${input_cram}.crai' && + @ADDTHREADS@ + ln -s '$input' input.cram && + #if str( $input.metadata.cram_index ) != "None": + ln -f -s '${input.metadata.cram_index}' input.cram.crai && #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 + @PREPARE_FASTA_IDX@ samtools view #if $parameter_regions.target_region == "regions_bed_file" - -L '${parameter_regions.regions_bed_file}' + -L '$parameter_regions.regions_bed_file' #end if - -@ \${GALAXY_SLOTS:-2} + -@ \$addthreads -b - -T '$ref_fa' + -T '$reffa' -o '$output_alignment' - '$input_cram' + input.cram #if $parameter_regions.target_region == "region" - '${parameter_regions.region_string}' + '$parameter_regions.region_string' #end if ]]></command> <inputs> - <param name="input_alignment" type="data" format="cram" label="CRAM alignment file"/> - <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="input_reference" type="select" label="Reference genome"> - <options from_data_table="fasta_indexes"> - <filter type="data_meta" ref="input_alignment" key="dbkey" column="dbkey" /> - </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="Reference FASTA file"/> - </when> - </conditional> + <param name="input" type="data" format="cram" label="CRAM alignment file"/> + <expand macro="mandatory_reference" argument="-t"/> <conditional name="parameter_regions"> <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)"> <option value="entire_input_file">Entire BAM alignment file</option> @@ -77,36 +56,33 @@ <tests> <test> - <param name="input_alignment" value="test.cram" ftype="cram" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> - - <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" /> + <param name="input" value="test.cram" ftype="cram" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> + <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" /> </test> <test> - <param name="input_alignment" value="test.cram" ftype="cram" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.cram" ftype="cram" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="region" /> <param name="region_string" value="CHROMOSOME_I" /> - - <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" /> </test> <test> - <param name="input_alignment" value="test.cram" ftype="cram" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.cram" ftype="cram" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="regions_bed_file" /> <param name="regions_bed_file" value="test.bed" ftype="bed" /> - - <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" /> </test> <test> - <param name="input_alignment" value="test2.cram" dbkey="equCab2" ftype="cram" /> - <param name="reference_source_selector" value="cached" /> - <param name="input_reference" value="equCab2chrM" /> + <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" /> + <param name="addref_select" value="cached" /> + <param name="ref" value="equCab2chrM" /> <param name="target_region" value="entire_input_file" /> - <output name="output_alignment" file="sam_to_bam_out2.bam" compare="sim_size" delta="250" /> + <output name="output_alignment" file="sam_to_bam_out2.bam" ftype="bam" lines_diff="4" /> </test> </tests>