bcftools_plugin_impute_info: macros.xml comparison

comparison macros.xml @ 4:c6071203aaa0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7

author	iuc
date	Sat, 11 Mar 2017 18:02:08 -0500
parents	35f66846632e
children	a15210afaf1d

comparison

equal deleted inserted replaced

-:35f66846632e
+:c6071203aaa0
 <macros>
-<token name="@VERSION@">1.3</token>
+<token name="@VERSION@">1.3.1</token>
 <xml name="stdio">
 <stdio>
 <exit_code range="1:" />
 <exit_code range=":-1" />
 <regex match="Error:" />
 <regex match="Exception:" />
 </stdio>
 </xml>
 <xml name="requirements">
 <requirements>
-<requirement type="package" version="1.3">bcftools</requirement>
+<requirement type="package" version="1.3.1">bcftools</requirement>
 <!-- conda dependency -->
-<requirement type="package" version="1.3">htslib</requirement>
+<requirement type="package" version="1.3.2">htslib</requirement>
-<!-- htslib provides tabix and bgzip
+<yield />
-<requirement type="package" version="0.2.6">tabix</requirement>
--->
-<requirement type="package" version="1.2">samtools</requirement>
 </requirements>
 </xml>
 <xml name="version_command">
 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
 </xml>
 <token name="@PREPARE_INPUT_FILE@">
 <![CDATA[
 ## May need to symlink input if there is an associated
 #set $input_vcf = 'input.vcf.gz'
 #if $input_file.is_of_type('vcf')
-bgzip -c "$input_file" > $input_vcf &&
+bgzip -c '$input_file' > $input_vcf &&
 bcftools index $input_vcf &&
 #elif $input_file.is_of_type('vcf_bgzip')
-ln -s "$input_file" $input_vcf
+ln -s '$input_file' $input_vcf
 #elif $input_file.is_of_type('bcf')
 #set $input_vcf = 'input.bcf'
-ln -s "$input_file" $input_vcf &&
+ln -s '$input_file' $input_vcf &&
 #if $input_file.metadata.bcf_index:
-ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
+ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
 #else
 bcftools index $input_vcf &&
 #end if
 #elif $input_file.is_of_type('bcf_bgzip')
-ln -s "$input_file" $input_vcf
+ln -s '$input_file' $input_vcf
 #end if
 ]]>
 </token>
 <token name="@INPUT_FILE@">
 $input_vcf
 <token name="@PREPARE_INPUT_FILES@">
 <![CDATA[
 ## May need to symlink input if there is an associated
 #set $input_vcfs = []
 #set $vcfs_list_file = 'vcfs_list'
-#for (i,input_file) in enumerate($input_files):
+#for (i, input_file) in enumerate($input_files):
 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
 #if $input_file.is_of_type('vcf')
-bgzip -c "$input_file" > $input_vcf &&
+bgzip -c '$input_file' > $input_vcf &&
 bcftools index $input_vcf &&
 #elif $input_file.is_of_type('vcf_bgz')
-ln -s "$input_file" $input_vcf
+ln -s '$input_file' $input_vcf
 #elif $input_file.is_of_type('bcf')
 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
-## bgzip -c "$input_file" > $input_vcf &&
+ln -s '$input_file' $input_vcf &&
-ln -s "$input_file" $input_vcf &&
 #if $input_file.metadata.bcf_index:
-ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
+ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
 #else
 bcftools index $input_vcf &&
 #end if
 #elif $input_file.is_of_type('bcfvcf_bgz')
-ln -s "$input_file" $input_vcf &&
+ln -s '$input_file' $input_vcf &&
 #end if
 echo '$input_vcf' >> $vcfs_list_file &&
 $input_vcfs.append($input_vcf)
 #end for
 ]]>
 <token name="@INPUT_LIST_FILE@">
 $vcfs_list_file
 </token>
 <xml name="macro_fasta_ref">
-<param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" />
+<param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
 </xml>
 <token name="@PREPARE_FASTA_REF@">
 <![CDATA[
 #set $input_fa_ref = None
 #if 'fasta_ref' in $section and $section.fasta_ref:
 #set $input_fa_ref = 'ref.fa'
-ln -s $section.fasta_ref $input_fa_ref &&
+ln -s '$section.fasta_ref' $input_fa_ref &&
 samtools faidx $input_fa_ref &&
 #end if
 ]]>
 </token>
 <token name="@FASTA_REF@">
 #if $input_fa_ref is not None:
---fasta-ref  "$input_fa_ref"
+--fasta-ref $input_fa_ref
 #elif 'fasta_ref' in $section and $section.fasta_ref:
---fasta-ref "${section.fasta_ref}"
+--fasta-ref '${section.fasta_ref}'
 #end if
 </token>
 <xml name="macro_ref_fasta">
 <conditional name="reference_source">
 </conditional>
 </xml>
 <xml name="macro_AF_file">
-<param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" />
+<param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
 </xml>
 <!-- This may need to bgzip and tabix the file -->
 <token name="@PREPARE_AF_FILE@">
 <![CDATA[
 #if 'AF_file' in $section and $section.AF_file:
 #pass
 #end if
 ]]>
 </token>
 <token name="@AF_FILE@">
 #if 'AF_file' in $section and $section.AF_file:
---AF-file "${section.AF_file}"
+--AF-file '${section.AF_file}'
 #end if
 </token>
 <xml name="macro_estimate_AF">
-<param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
+<param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
 </xml>
 <token name="@ESTIMATE_AF@">
 #if 'estimate_AF' in $section and $section.estimate_AF:
 --estimate-AF "${section.estimate_AF}"
 #end if
 <yield/>
 </param>
 </xml>
 <token name="@COLLAPSE@">
 #if $section.collapse:
---collapse "${section.collapse}"
+--collapse ${section.collapse}
 #end if
 </token>
 <xml name="macro_apply_filters">
 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
 </param>
 </xml>
 <token name="@APPLY_FILTERS@">
 #if $section.apply_filters:
---apply-filters "${section.apply_filters}"
+--apply-filters '${section.apply_filters}'
 #end if
 </token>
 <xml name="macro_select_output_type">
 <param name="output_type" type="select">
 </when>
 </conditional>
 </xml>
 <token name="@REGIONS@">
 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
---regions "$section.regions.regions"
+--regions '$section.regions.regions'
 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
---regions-file "$section.regions.regions_file"
+--regions-file '$section.regions.regions_file'
 #end if
 </token>
 <xml name="macro_targets_file">
 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
 <![CDATA[
 #if $targets_path:
 --targets-file "${section.targets.invert_targets_file}${targets_path}"
 #else:
 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
---targets "${section.targets.invert_targets_file}${section.targets.targets}"
+--targets '${section.targets.invert_targets_file}${section.targets.targets}'
 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
 #end if
 #end if
 ]]>
 </xml>
 <token name="@SAMPLES@">
 #set $samples_defined = False
 #if str($section.samples) != '':
 #set $samples_defined = True
---samples "${section.invert_samples}${section.samples}"
+--samples '${section.invert_samples}${section.samples}'
 #end if
 #if $section.samples_file:
 #set $samples_defined = True
 --samples-file "${section.invert_samples_file}${section.samples_file}"
 #end if
 <xml name="macro_sample">
 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
 </xml>
 <token name="@SAMPLE@">
 #if $section.sample:
---sample "${section.sample}"
+--sample '${section.sample}'
 #end if
 </token>
 <xml name="macro_include">
 <validator type="regex" message="COLUMN names  separated by commas">^([^,]+(,[^,]+)*)?$</validator>
 </param>
 </xml>
 <token name="@COLUMNS@">
 #if $section.columns != '':
---columns "${section.columns}"
+--columns '${section.columns}'
 #end if
 </token>
 <xml name="macro_haploid2diploid">
 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
 and VCF<->BCF conversion.
 This Galaxy tool recommends using the compressed BCF format
 as piping is not implemented, and uncompressed data would
 use unnecessary amounts of space.
+]]></token>
-]]></token>
 <token name="@REGIONS_HELP@">
 <![CDATA[
 Region Selections
 -----------------
 chromosomes, the VCF will always be processed in ascending
 genomic coordinate order no matter what order they appear in
 FILE. Note that overlapping regions in FILE can result in
 duplicated out of order positions in the output. This option
 requires indexed VCF/BCF files.
+]]></token>
-]]></token>
 <token name="@TARGETS_HELP@"><![CDATA[
 Targets
 -------
 Similar to regions, but the next position is accessed by streaming the whole
 | both       | abbreviation of "-c indels  -c snps"                           |
 +------------+----------------------------------------------------------------+
 | id         | only records with identical ID column are compatible.          |
 |            | Supportedby bcftools merge only.                               |
 +------------+----------------------------------------------------------------+
 </token>
 <token name="@EXPRESSIONS_HELP@">
 <![CDATA[
 Expressions
 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
 MIN(DP)>35 && AVG(GQ)>50
 ID=@file       .. selects lines with ID present in the file
 ID!=@~/file    .. skip lines with ID present in the ~/file
 MAF[0]<0.05    .. select rare variants at 5% cutoff
+]]></token>
-]]></token>
 </macros>

Mercurial > repos > iuc > bcftools_plugin_impute_info

comparison macros.xml @ 4:c6071203aaa0 draft