| Previous changeset 3:e86fcef8ed91 (2020-09-01) Next changeset 5:19f3b583a9b3 (2020-10-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332" |
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modified:
macros.xml variant.xml |
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| diff -r e86fcef8ed91 -r 2308bc523659 macros.xml --- a/macros.xml Tue Sep 01 03:08:24 2020 -0400 +++ b/macros.xml Tue Oct 13 16:00:16 2020 +0000 |
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| @@ -5,7 +5,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">medaka</requirement> - <requirement type="package" version="1.4.1">scipy</requirement> + <yield /> </requirements> </xml> <xml name="version_command"> |
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| diff -r e86fcef8ed91 -r 2308bc523659 variant.xml --- a/variant.xml Tue Sep 01 03:08:24 2020 -0400 +++ b/variant.xml Tue Oct 13 16:00:16 2020 +0000 |
| [ |
| @@ -1,40 +1,75 @@ <?xml version="1.0"?> -<tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>Probability decoding</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package" version="1.4.1">scipy</requirement> + </expand> + <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ ## initialize @REF_FASTA@ -## run -medaka variant -## optional ---debug -#if $region - --region '${region}' + +#if $pool.pool_mode == "Yes": + ## run + medaka variant + ## optional + --debug + #if $regions + --regions '${regions}' + #end if + $verbose + ## required + reference.fa + #for $current in $pool.inputs + '$current' + #end for + '$out_result' ## output + + 2>&1 | tee '$out_log' +#elif $pool.pool_mode == "No": + ## run + medaka variant + ## optional + --debug + #if $regions + --regions '${regions}' + #end if + $verbose + ## required + reference.fa + '$pool.input' + '$out_result' ##output + 2>&1 | tee '$out_log' #end if -$verbose -## required -reference.fa -#for $current in $inputs - '$current' -#end for -'$out_result' ## output - -2>&1 | tee '$out_log' #if $out_annotated - && python '$__tool_directory__/annotateVCF.py' '$out_result' '$in_mpileup' '$out_annotated' + && samtools faidx reference.fa + && grep -v "^#" '$out_result' > tmp.txt + && cut -f 1,2 tmp.txt > positions.txt + && samtools mpileup -d 0 --positions positions.txt -Q $output_annotated.min_basequal -q $output_annotated.min_mapqual -f reference.fa '$output_annotated.in_bam' > mpileup.txt + && python '$__tool_directory__/annotateVCF.py' '$out_result' mpileup.txt '$out_annotated' #end if ]]></command> <inputs> - <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/> + <conditional name="pool"> + <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?"> + <option value="No" selected="True">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/> + </when> + <when value="No"> + <param name="input" type="data" format="h5" label="Select consensus file(s)"/> + </when> + </conditional> <expand macro="reference"/> - <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','."> + <param argument="--regions" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','."> <sanitizer invalid_char=""> <valid initial="string.ascii_letters,string.digits"> <add value="_"/> @@ -44,15 +79,17 @@ </sanitizer> </param> <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/> - <conditional name="output_annotated"> - <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires pileup file)"> + <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)"> <option value="true" selected="true">Output annotated VCF</option> <option value="false">Don't output annotated VCF</option> </param> <when value="true"> - <param name="in_mpileup" type = "data" format="pileup" optional="false" label="Mpileup to annotate the VCF"/> + <param name="in_bam" type="data" format="bam" optional="false" label="BAM to annotate the VCF" /> + <param name="min_basequal" type="integer" value="0" min="0" max="50" label="Minimum base quality" help="The minimum base quality (default: 0) at a given variant position required to include a read in the calculation of variant statistics (samtools mpileup -Q)" /> + <param name="min_mapqual" type="integer" value="0" min="0" max="60" label="Minimum mapping quality" help="The minimum mapping quality (default: 0) required for a read to be considered in calculation of variant statistics (samtools mpileup -q)" /> </when> + <when value="false"/> </conditional> <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/> </inputs> @@ -70,14 +107,54 @@ <tests> <!-- #1 default --> <test expect_num_outputs="3"> - <param name="inputs" value="medaka_test.hdf"/> + <conditional name="pool"> + <param name="pool_mode" value="Yes"/> + <param name="inputs" value="medaka_test.hdf,medaka_test.hdf"/> + </conditional> <conditional name="reference_source"> <param name="reference_source_selector" value="history"/> <param name="ref_file" value="ref.fasta"/> </conditional> <conditional name="output_annotated"> <param name="output_annotated_select" value="true"/> - <param name="in_mpileup" value="annotate_vcf_test.pileup"/> + <param name="in_bam" value="medaka_test.bam"/> + </conditional> + <param name="output_log_bool" value="true"/> + + <output name="out_result"> + <assert_contents> + <has_n_lines n="9"/> + <has_line line="##fileformat=VCFv4.1" /> + <has_line line="##medaka_version=1.0.3" /> + </assert_contents> + </output> + <output name="out_annotated"> + <assert_contents> + <has_n_lines n="16"/> + <has_line line="##fileformat=VCFv4.1" /> + <has_line line="##medaka_version=1.0.3" /> + <has_line line="##annotateVCFVersion=0.1" /> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_n_lines n="10" /> + </assert_contents> + </output> + </test> + <!--No pooling--> + <test expect_num_outputs="3"> + <conditional name="pool"> + <param name="pool_mode" value="No"/> + <param name="input" value="medaka_test.hdf"/> + </conditional> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="ref.fasta"/> + </conditional> + <conditional name="output_annotated"> + <param name="output_annotated_select" value="true"/> + <param name="in_bam" value="medaka_test.bam"/> </conditional> <param name="output_log_bool" value="true"/> |