diff macros.xml @ 4:c6071203aaa0 draft

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

--- a/macros.xml	Tue Jan 31 12:44:53 2017 -0500
+++ b/macros.xml	Sat Mar 11 18:02:08 2017 -0500
@@ -1,6 +1,5 @@
-
 <macros>
-  <token name="@VERSION@">1.3</token>
+  <token name="@VERSION@">1.3.1</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -11,13 +10,10 @@
   </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>
-      <!-- htslib provides tabix and bgzip
-      <requirement type="package" version="0.2.6">tabix</requirement>
-      -->
-      <requirement type="package" version="1.2">samtools</requirement>
+      <requirement type="package" version="1.3.2">htslib</requirement>
+      <yield />
     </requirements>
   </xml>
   <xml name="version_command">
@@ -48,20 +44,20 @@
 ## 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>
@@ -77,24 +73,23 @@
 ## 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)
@@ -109,23 +104,23 @@
   </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>
 
@@ -151,24 +146,24 @@
 
 
   <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
+    #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:
@@ -222,7 +217,7 @@
   </xml>
   <token name="@COLLAPSE@">
 #if $section.collapse:
-  --collapse "${section.collapse}"
+  --collapse ${section.collapse}
 #end if
   </token>
 
@@ -234,7 +229,7 @@
   </xml>
   <token name="@APPLY_FILTERS@">
 #if $section.apply_filters:
-  --apply-filters "${section.apply_filters}"
+  --apply-filters '${section.apply_filters}'
 #end if
   </token>
 
@@ -286,9 +281,9 @@
   </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>
 
@@ -351,7 +346,7 @@
   --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
@@ -375,7 +370,7 @@
 #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
@@ -388,7 +383,7 @@
   </xml>
   <token name="@SAMPLE@">
 #if $section.sample:
-  --sample "${section.sample}"
+  --sample '${section.sample}'
 #end if
   </token>
 
@@ -425,7 +420,7 @@
   </xml>
   <token name="@COLUMNS@">
 #if $section.columns != '':
-  --columns "${section.columns}"
+  --columns '${section.columns}'
 #end if
   </token>
 
@@ -453,8 +448,7 @@
 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
@@ -475,8 +469,7 @@
 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
 -------
@@ -541,7 +534,6 @@
 | id         | only records with identical ID column are compatible.          |
 |            | Supportedby bcftools merge only.                               |
 +------------+----------------------------------------------------------------+
-
   </token>
 
   <token name="@EXPRESSIONS_HELP@">
@@ -666,10 +658,5 @@
       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>