Repository 'bcftools_csq'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq

Changeset 18:9f69e7d58d03 (2025-12-02)
Previous changeset 17:d237eaef451f (2024-08-18)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
modified:
bcftools_csq.xml
macros.xml
b
diff -r d237eaef451f -r 9f69e7d58d03 bcftools_csq.xml
--- a/bcftools_csq.xml Sun Aug 18 10:00:41 2024 +0000
+++ b/bcftools_csq.xml Tue Dec 02 08:13:25 2025 +0000
[
b'@@ -4,13 +4,12 @@\n         <token name="@EXECUTABLE@">csq</token>\n         <import>macros.xml</import>\n     </macros>\n-    <expand macro="bio_tools" />\n+    <expand macro="bio_tools"/>\n     <expand macro="requirements">\n         <expand macro="samtools_requirement"/>\n     </expand>\n-    <expand macro="version_command" />\n+    <expand macro="version_command"/>\n     <command detect_errors="aggressive"><![CDATA[\n-@PREPARE_ENV@\n @PREPARE_INPUT_FILE@\n #set $section = $sec_required.reference_source\n @PREPARE_FASTA_REF@\n@@ -40,6 +39,9 @@\n #if str($sec_csq_opts.trim_protein_seq)\n     --trim-protein-seq $sec_csq_opts.trim_protein_seq\n #end if\n+#if $sec_csq_opts.genetic_code\n+    --genetic-code \'$sec_csq_opts.genetic_code\'\n+#end if\n \n ## Subset section\n #set $section = $sec_subset\n@@ -61,104 +63,149 @@\n ]]>\n     </command>\n     <inputs>\n-        <expand macro="macro_input" />\n+        <expand macro="macro_input"/>\n         <section name="sec_required" expanded="true" title="Required References">\n-            <expand macro="macro_fasta_ref" />\n-            <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" \n-                 help="From Ensembl:  ftp://ftp.ensembl.org/pub/current_gff3/"/>\n+            <expand macro="macro_fasta_ref"/>\n+            <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" help="From Ensembl:  ftp://ftp.ensembl.org/pub/current_gff3/"/>\n         </section>\n         <section name="sec_csq_opts" expanded="true" title="CSQ Options">\n-            <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site"\n-                help="-ncsq 16"/>\n-            <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time"\n-                 help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>\n-            <param name="phase" type="select" optional="true" label="phase" \n-                 help="how to construct haplotypes and how to deal with unphased data">\n-                <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option>\n-                <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option>\n+            <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site" help="-ncsq 16"/>\n+            <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time" help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>\n+            <param name="phase" type="select" optional="true" label="phase" help="how to construct haplotypes and how to deal with unphased data">\n+                <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -&gt; 0|1)</option>\n+                <option value="m">merge *all* GTs into a single haplotype (0/1 -&gt; 1, 1/2 -&gt; 1)</option>\n                 <option value="r">require phased GTs, throw an error on unphased het GTs</option>\n-                <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option>\n+                <option value="R">create non-reference haplotypes if possible (0/1 -&gt; 1|1, 1/2 -&gt; 1|2)</option>\n                 <option value="s">skip unphased GTs</option>\n             </param>\n-            <param name="custom_tag" type="text" value="" optional="true" \n-                 label="use this custom tag to store consequences rather than the default BCSQ tag">\n-                 <validator type="regex" message="">^(\\w+)?$</validator>\n+            <param name="custom_tag" type="text" value="" optional="true" label="use this custom t'..b'st_using_reference" select_from="cached" ref="csq" />\n-            <param name="gff_annot" ftype="gff3" value="csq.gff3" />\n-            <param name="output_type" value="v" />\n+            <param name="input_file" ftype="vcf" value="csq.vcf"/>\n+            <section name="sec_required">\n+                <expand macro="test_using_reference" select_from="cached" ref="csq"/>\n+            </section>\n+            <section name="sec_required">\n+                <param name="gff_annot" ftype="gff3" value="csq.gff3"/>\n+            </section>\n+            <param name="output_type" value="v"/>\n             <output name="output_file">\n                 <assert_contents>\n-                    <has_text text="BCSQ" />\n+                    <has_text text="BCSQ"/>\n                 </assert_contents>\n             </output>\n         </test>\n         <!-- Test protein seq prediction-->\n         <test>\n-            <param name="input_file" ftype="vcf" value="csq.vcf" />\n-            <expand macro="test_using_reference" select_from="cached" ref="csq" />\n-            <param name="gff_annot" ftype="gff3" value="csq.gff3" />\n-            <param name="output_type" value="v" />\n+            <param name="input_file" ftype="vcf" value="csq.vcf"/>\n+            <section name="sec_required">\n+                <expand macro="test_using_reference" select_from="cached" ref="csq"/>\n+            </section>\n+            <section name="sec_required">\n+                <param name="gff_annot" ftype="gff3" value="csq.gff3"/>\n+            </section>\n+            <param name="output_type" value="v"/>\n             <section name="sec_csq_opts">\n                 <param name="trim_protein_seq" value="10"/>\n+                <param name="genetic_code" value="1"/>\n             </section>\n             <output name="output_file">\n                 <assert_contents>\n-                    <has_text text="BCSQ" />\n+                    <has_text text="BCSQ"/>\n                 </assert_contents>\n             </output>\n             <assert_command>\n-                <has_text text="--trim-protein-seq" />\n+                <has_text text="--trim-protein-seq"/>\n+                <has_text text="--genetic-code \'1\'"/>\n             </assert_command>\n         </test>\n         <!-- Test region overlap-->\n         <test>\n-            <param name="input_file" ftype="vcf" value="csq.vcf" />\n-            <expand macro="test_using_reference" select_from="cached" ref="csq" />\n-            <param name="gff_annot" ftype="gff3" value="csq.gff3" />\n-            <param name="output_type" value="v" />\n+            <param name="input_file" ftype="vcf" value="csq.vcf"/>\n+            <section name="sec_required">\n+                <expand macro="test_using_reference" select_from="cached" ref="csq"/>\n+            </section>\n+            <section name="sec_required">\n+                <param name="gff_annot" ftype="gff3" value="csq.gff3"/>\n+            </section>\n+            <param name="output_type" value="v"/>\n             <section name="sec_restrict">\n-                <param name="regions_overlap" value="1"/>\n+                <conditional name="regions">\n+                    <param name="regions_src" value="regions" />\n+                    <repeat name="region_specs">\n+                        <param name="chrom" value="1" />\n+                    </repeat>\n+                </conditional>\n             </section>\n             <output name="output_file">\n                 <assert_contents>\n-                    <has_text text="BCSQ" />\n+                    <has_text text="BCSQ"/>\n                 </assert_contents>\n             </output>\n             <assert_command>\n-                <has_text text="--regions-overlap" />\n+                <has_text text="--regions-overlap"/>\n             </assert_command>\n         </test>\n     </tests>\n@@ -197,8 +244,8 @@\n \n @BCFTOOLS_MANPAGE@#@EXECUTABLE@\n \n-@BCFTOOLS_WIKI@\n+@BCFTOOLS_HOWTOS@\n ]]>\n     </help>\n-    <expand macro="citations" />\n+    <expand macro="citations"/>\n </tool>\n'
b
diff -r d237eaef451f -r 9f69e7d58d03 macros.xml
--- a/macros.xml Sun Aug 18 10:00:41 2024 +0000
+++ b/macros.xml Tue Dec 02 08:13:25 2025 +0000
[
b'@@ -1,7 +1,7 @@\n <macros>\n-  <token name="@TOOL_VERSION@">1.15.1</token>\n-  <token name="@VERSION_SUFFIX@">4</token>\n-  <token name="@PROFILE@">20.01</token>\n+  <token name="@TOOL_VERSION@">1.22</token>\n+  <token name="@VERSION_SUFFIX@">0</token>\n+  <token name="@PROFILE@">24.1</token>\n   <xml name="bio_tools">\n       <xrefs>\n           <xref type="bio.tools">bcftools</xref>\n@@ -10,15 +10,15 @@\n   <xml name="requirements">\n     <requirements>\n       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>\n-      <requirement type="package" version="1.15.1">htslib</requirement>\n+      <requirement type="package" version="1.22.1">htslib</requirement>\n       <yield />\n     </requirements>\n   </xml>\n   <xml name="samtools_requirement">\n-      <requirement type="package" version="1.15.1">samtools</requirement>\n+      <requirement type="package" version="1.22.1">samtools</requirement>\n   </xml>\n   <xml name="matplotlib_requirement">\n-      <requirement type="package" version="3.5.3">matplotlib</requirement>\n+      <requirement type="package" version="3.10.7">matplotlib</requirement>\n   </xml>\n   <xml name="version_command">\n     <version_command>bcftools 2&gt;&amp;1 | grep \'Version:\'</version_command>\n@@ -30,16 +30,11 @@\n       <yield />\n     </citations>\n   </xml>\n-  <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>\n-  <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>\n+  <token name="@BCFTOOLS_HOWTOS@">https://samtools.github.io/bcftools/howtos/index.html</token>\n+  <token name="@BCFTOOLS_MANPAGE@">https://www.htslib.org/doc/bcftools.html</token>\n   <token name="@THREADS@">\n   --threads \\${GALAXY_SLOTS:-4}\n   </token>\n-  <token name="@PREPARE_ENV@">\n-<![CDATA[\n-export BCFTOOLS_PLUGINS=`which bcftools | sed \'s,bin/bcftools,libexec/bcftools,\'`;\n-]]>\n-  </token>\n   <xml name="macro_input">\n     <!-- \n     REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files\n@@ -294,8 +289,8 @@\n     help="inverts the query/filtering applied by the targets" />\n   </xml>\n \n-  <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">\n-    <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">\n+  <xml name="macro_restriction_spec" tokens="type,label_type">\n+    <repeat name="@TYPE@_specs" title="@LABEL_TYPE@ Filter" default="1" min="1">\n         <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">\n             <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>\n         </param>\n@@ -305,36 +300,85 @@\n         <param name="stop" type="text" label="@LABEL_TYPE@ end position">\n             <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>\n         </param>\n-        <yield />\n     </repeat>\n   </xml>\n \n-  <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">\n+  <xml name="macro_restrictions_file" tokens="type,label_type">\n     <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />\n   </xml>\n \n-  <xml name="macro_restrict" token_type="region" token_label_type="Region" >\n+  <xml name="__macro_restrict__" tokens="type,label_select,label_type,pos_is_default,rec_is_default">\n     <conditional name="@TYPE@s">\n-        <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">\n-            <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>\n-            <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>\n-            <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>\n+      <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@">\n+        <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>\n+        <option value="@TYPE@s">Specify one or more @LABEL_TYPE@'..b'intervals = $section.targets.target_specs\n+    @PARSE_INTERVALS@\n+    --targets \'${section.targets.invert_targets_file}$intervals_spec\'\n+  #elif $section.targets.targets_src == \'targets_file\':\n+    #if $targets_path:\n+      --targets-file \'${section.targets.invert_targets_file}${targets_path}\'\n+    #else:\n+      --targets-file \'${section.targets.invert_targets_file}${section.targets.targets_file}\'\n+    #end if\n+  #end if\n+  #if \'targets_overlap\' in $section.targets:\n+    --targets-overlap $section.targets.targets_overlap\n+  #end if\n #end if\n ]]>\n   </token>\n@@ -417,7 +462,7 @@\n <![CDATA[\n #set $regions_path = None\n #if \'regions\' in $section\n-  #if $section.regions.regions_src == \'regions_file\' and $section.regions.regions_file:\n+  #if $section.regions.regions_src == \'regions_file\':\n     #if $section.regions.regions_file.ext.startswith(\'bed\'):\n       #set $regions_path = \'regions_file.bed\'\n       ln -s \'$section.regions.regions_file\' $regions_path &&\n@@ -461,11 +506,31 @@\n       </param>\n       <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"\n              help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />\n-      <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"\n-             help="File of samples to include" />\n+      <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" help="File of samples to include" />\n       <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"\n              help="inverts the query/filtering applied by Samples file" />\n   </xml>\n+\n+  <xml name="macro_samples_enhanced" token_all_samples="" token_file_help="File listing samples to include one per line.">\n+      <conditional name="specify_samples">\n+          <param name="how" type="select" label="How do you want to select samples?">\n+              <option value="-s">Specify samples manually</option>\n+              <option value="-S">Provide sample file</option>\n+              <option value="@ALL_SAMPLES@" selected="true">No selection; just use all samples found in input</option>\n+          </param>\n+          <when value="-s">\n+              <param argument="--samples" name="samples_spec" type="text" optional="false" label="Sample(s)" help="Specify a single sample by name or a comma-separated list of sample names.">\n+                <validator type="expression" message="Please specify a single sample by name or a comma-separated list of sample names">value.strip() and value[0] not in "^," and ",," not in value</validator>\n+              </param>\n+              <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude these samples instead of including them?" help="Equivalent to prefixing the list of samples with &quot;^&quot; on the command line."/>\n+          </when>\n+          <when value="-S">\n+              <param argument="--samples_file" type="data" format="tabular" optional="@IS_OPTIONAL@" label="Samples file" help="@FILE_HELP@" />\n+              <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude the samples listed in the file instead of including them?" help="Equivalent to prefixing the file with &quot;^&quot; on the command line."/>\n+          </when>\n+          <when value="@ALL_SAMPLES@" />\n+      </conditional>\n+  </xml>\n   <token name="@SAMPLES@">\n #set $samples_defined = False\n #if str($section.samples) != \'\':\n@@ -478,8 +543,8 @@\n #end if\n   </token>\n \n-  <xml name="macro_sample">\n-      <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />\n+  <xml name="macro_sample" token_help="Apply variants of the given sample">\n+      <param name="sample" type="text" optional="true" label="Sample" help="@HELP@" />\n   </xml>\n   <token name="@SAMPLE@">\n #if $section.sample:\n'