| Previous changeset 12:329deb17a9f7 (2021-11-27) Next changeset 14:b61f5d6a7f25 (2023-11-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 1354b1358df89a922c3243f7e27ce789094b8644" |
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modified:
samtools_mpileup.xml |
| b |
| diff -r 329deb17a9f7 -r 9da0311ab1dd samtools_mpileup.xml --- a/samtools_mpileup.xml Sat Nov 27 12:32:35 2021 +0000 +++ b/samtools_mpileup.xml Sun Dec 19 15:57:35 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.5" profile="@PROFILE@"> +<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.6" profile="@PROFILE@"> <description>multi-way pileup of variants</description> <macros> <import>macros.xml</import> @@ -37,7 +37,7 @@ #end if #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": - -G '$excluded_read_groups' + -G '$$advanced_options.exclude_read_group.group_paste' #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history" -G '$advanced_options.exclude_read_group.read_groups' #end if @@ -69,21 +69,21 @@ <expand macro="mandatory_reference" argument="-f"/> <conditional name="advanced_options"> <param name="advanced_options_selector" type="select" label="Set advanced options"> - <option selected="True" value="default">Basic</option> + <option selected="true" value="default">Basic</option> <option value="advanced">Advanced</option> </param> <when value="default" /> <when value="advanced"> <conditional name="filter_by_flags"> <param name="filter_flags" type="select" label="Set filter by flags"> - <option selected="True" value="nofilter">Do not filter</option> + <option selected="true" value="nofilter">Do not filter</option> <option value="filter">Filter by flags to exclude or require</option> </param> <when value="filter"> - <param name="require_flags" argument="--rf/--incl-flags" type="select" multiple="True" display="checkboxes" label="Require"> + <param name="require_flags" argument="--rf/--incl-flags" type="select" multiple="true" display="checkboxes" label="Require"> <expand macro="flag_options" /> </param> - <param name="exclude_flags" argument="--ff/--excl-flags" type="select" multiple="True" display="checkboxes" label="Exclude"> + <param name="exclude_flags" argument="--ff/--excl-flags" type="select" multiple="true" display="checkboxes" label="Exclude"> <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/> </param> </when> @@ -91,7 +91,7 @@ </conditional> <conditional name="limit_by_region"> <param name="limit_by_regions" type="select" label="Select regions to call"> - <option selected="True" value="no_limit">Do not limit</option> + <option selected="true" value="no_limit">Do not limit</option> <option value="limit">Specify regions</option> </param> <when value="limit"> @@ -106,7 +106,7 @@ <conditional name="exclude_read_group"> <param name="exclude_read_groups" argument="-R/--exclude-RG" type="select" label="Select read groups to exclude"> - <option selected="True" value="no_limit">Do not exclude</option> + <option selected="true" value="no_limit">Do not exclude</option> <option value="history">From a text file</option> <option value="paste">Paste a list of read groups</option> </param> @@ -133,7 +133,7 @@ </conditional> <conditional name="output_options_cond"> <param name="output_options_selector" type="select" label="Output options"> - <option selected="True" value="default">Default</option> + <option selected="true" value="default">Default</option> <option value="advanced">Advanced</option> </param> <when value="default"/> @@ -142,7 +142,7 @@ <param name="output_mapping_quality" argument="-s/--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" /> <param name="output_read_names" argument="--output-QNAME" type="boolean" truevalue="--output-QNAME" falsevalue="" checked="False" label="Output an extra column containing comma-separated read names. (--output-QNAME)" /> <param name="output_all_pos" argument="-a" type="select" label="Output absolutely all positions" help="Output all positions, including those with zero depth. (-a) Output absolutely all positions, including unused reference sequences (-aa). Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file."> - <option selected="True" value="">No</option> + <option selected="true" value="">No</option> <option value="-a">all (including those with zero depth)</option> <option value="-aa">absolutely all (including unused reference sequences)</option> </param> |