Mercurial > repos > avowinkel > gatk
diff gatk_macros.xml @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
| author | avowinkel |
|---|---|
| date | Thu, 24 Sep 2015 12:10:01 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk_macros.xml Thu Sep 24 12:10:01 2015 -0400 @@ -0,0 +1,166 @@ +<macros> + + <xml name="requirements"> + <requirements> + <requirement type="package">gatk</requirement> + <requirement type="set_environment">GATK_PATH</requirement> + <requirement type="set_environment">GATK_SITE_OPTIONS</requirement> + <requirement type="package" version="3.1.2.1">package_r_for_gatk_3_4_0</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command><![CDATA[ @GATK_EXEC@ --help|grep '^The Genome' ]]></version_command> + </xml> + + <token name="@VERSION@">3.4-0</token> + <token name="@OUTPUT_NAME_PREFIX@">${tool.name} - ${analysis_type.analysis_type_selector}</token> + <token name="@GATK_EXEC@"> +<![CDATA[ + #if $cond_threads.cond_threads_enabled: + #if int($cond_threads.nct) > 1: + THREAD_STRING="-nct $cond_threads.nct" && + #end if + #if int($cond_threads.nt) > 1: + THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" && + #end if + #if int($cond_threads.mem) > 0: + GATK_MEM=$cond_threads.mem && + #end if + #end if + java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-} +]]> + </token> + + <xml name="macro_vcf_input" tokens="tag"> + <param name="input" type="data" format="vcf" multiple="true" label="Variant files (VCF format)" help="-V, ‑‑variant"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> + </param> + </xml> + <token name="@token_vcf_input_pre@" tokens="tag"> +<![CDATA[ + ############################ + ## create links to gVCF input files with correct extensions + ############################ + #for $i, $variant in enumerate($analysis_type.input): + ln -s -f ${variant} variant_${i}.vcf && + #end for +]]> + </token> + <token name="@token_vcf_input@"> +<![CDATA[ + #for $i, $variant in enumerate($analysis_type.input): + --variant variant_${i}.vcf + #end for + @token_reference_input@ +]]> + </token> + + + <xml name="macro_gvcf_input" tokens="tag"> + <param name="input" type="data" format="vcf" multiple="true" label="Variant files (gVCF format)" help="-V, ‑‑variant"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> + </param> + </xml> + <token name="@token_gvcf_input_pre@" tokens="tag"> +<![CDATA[ + ############################ + ## create links to gVCF input files with correct extensions + ############################ + #for $i, $variant in enumerate($analysis_type.input): + ln -s -f ${variant} variant_${i}.g.vcf && + #end for +]]> + </token> + <token name="@token_gvcf_input@"> +<![CDATA[ + #for $i, $variant in enumerate($analysis_type.input): + --variant variant_${i}.g.vcf + #end for + @token_reference_input@ +]]> + </token> + + <xml name="macro_bam_input"> + <conditional name="cond_bam_input"> + <param name="all_in_one" type="boolean" value="false" label="Input all BAM files in a single command" /> + <when value="true"> + <param name="input" type="data" format="bam" multiple="true" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file"> + <validator type="unspecified_build"/> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/> + </param> + </when> + <when value="false"> + <param name="input" type="data" format="bam" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file"> + <validator type="unspecified_build"/> + <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/> + </param> + </when> + </conditional> + </xml> + <token name="@token_bam_input_pre@"> +<![CDATA[ + ############################ + ## create links to bam input files with correct extensions + ############################ + #if $analysis_type.cond_bam_input.all_in_one + #for $i, $bam in enumerate($analysis_type.cond_bam_input.input): + ln -s -f ${bam} input_${i}.bam && + ln -s -f ${bam.metadata.bam_index} input_${i}.bam.bai && + #end for + #else + ln -s -f ${analysis_type.cond_bam_input.input} input.bam && + ln -s -f ${analysis_type.cond_bam_input.input.metadata.bam_index} input.bam.bai && + #end if +]]> + </token> + <token name="@token_bam_input@"> +<![CDATA[ + #if $analysis_type.cond_bam_input.all_in_one + #for $i, $bam in enumerate($analysis_type.cond_bam_input.input): + --input_file input_${i}.bam + #end for + #else + --input_file input.bam + #end if + @token_reference_input@ +]]> + </token> + + <token name="@token_reference_input@"> +<![CDATA[ +]]> + </token> + <xml name="macro_input" tokens="tag"> + <yield /> + </xml> + + <xml name="macro_optional_parameters"> + <conditional name="optional_parameters"> + <param name="optional_parameters_enabled" type="boolean" label="Configure Optional Parameters" /> + <when value="true"> + <yield /> + </when> + <when value="false" /> + </conditional> + </xml> + + <xml name="macro_advanced_parameters"> + <conditional name="advanced_parameters"> + <param name="advanced_parameters_enabled" type="boolean" label="Configure Advanced Parameters" /> + <when value="true"> + <yield /> + </when> + <when value="false" /> + </conditional> + </xml> + + <xml name="macro_tests"> + <tests> + + </tests> + </xml> + +</macros>