| Previous changeset 18:48bbbcb692ce (2025-06-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_view commit 19dd8b645a77899ff98d139d79de824a23f416bb |
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modified:
macros.xml samtools_view.xml |
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| diff -r 48bbbcb692ce -r 5ec526530725 macros.xml --- a/macros.xml Thu Jun 19 13:02:07 2025 +0000 +++ b/macros.xml Wed Nov 12 12:59:47 2025 +0000 |
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| @@ -11,9 +11,9 @@ please only bump the minor version in order to let the requirement version catch up eventually). To find the tools check: `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` --> - <token name="@TOOL_VERSION@">1.21</token> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">22.05</token> + <token name="@TOOL_VERSION@">1.22</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">24.0</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 #if $filter @@ -167,6 +167,18 @@ <xml name="seed_input"> <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> + + <!-- Include/exclude by flags + flag options --> + <xml name="inclusive_filter_macro" token_argument=""> + <param name="inclusive_filter" argument="@ARGUMENT@" type="select" multiple="True" label="Require that these flags are set"> + <expand macro="flag_options" /> + </param> + </xml> + <xml name="exclusive_filter_macro" token_argument=""> + <param name="exclusive_filter" argument="@ARGUMENT@" type="select" multiple="True" label="Exclude reads with any of the following flags set"> + <expand macro="flag_options" /> + </param> + </xml> <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> <option value="1" selected="@S1@">Read is paired</option> <option value="2" selected="@S2@">Read is mapped in a proper pair</option> |
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| diff -r 48bbbcb692ce -r 5ec526530725 samtools_view.xml --- a/samtools_view.xml Thu Jun 19 13:02:07 2025 +0000 +++ b/samtools_view.xml Wed Nov 12 12:59:47 2025 +0000 |
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| @@ -321,12 +321,9 @@ <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." /> <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" /> <param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." /> - <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> - <expand macro="flag_options" /> - </param> - <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set"> - <expand macro="flag_options" /> - </param> + <!-- Use macro for inclusive and axclusive flags --> + <expand macro="inclusive_filter_macro" token_argument="-f"/> + <expand macro="exclusive_filter_macro" token_argument="-F"/> <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> <expand macro="flag_options" /> </param> |