Mercurial > repos > devteam > bowtie2
diff bowtie2_macros.xml @ 33:f76cbb84d67f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
| author | iuc |
|---|---|
| date | Wed, 24 Sep 2025 13:37:14 +0000 |
| parents | d5ceb9f3c25b |
| children |
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--- a/bowtie2_macros.xml Mon May 13 13:49:14 2024 +0000 +++ b/bowtie2_macros.xml Wed Sep 24 13:37:14 2025 +0000 @@ -1,6 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">2.5.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.5.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@"> @@ -59,7 +60,7 @@ #if $use_rg #if $rg_param('read_group_id_conditional') is None #set $rg_id = $rg_auto_name - #elif $rg_param('read_group_id_conditional').do_auto_name + #elif $rg_param('read_group_id_conditional').do_auto_name == "yes" #set $rg_id = $rg_auto_name #else #set $rg_id = str($rg_param('read_group_id_conditional').ID) @@ -67,7 +68,7 @@ #if $rg_param('read_group_sm_conditional') is None #set $rg_sm = '' - #elif $rg_param('read_group_sm_conditional').do_auto_name + #elif $rg_param('read_group_sm_conditional').do_auto_name == "yes" #set $rg_sm = $rg_auto_name #else #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) @@ -81,7 +82,7 @@ #if $rg_param('read_group_lb_conditional') is None #set $rg_lb = '' - #elif $rg_param('read_group_lb_conditional').do_auto_name + #elif $rg_param('read_group_lb_conditional').do_auto_name == "yes" #set $rg_lb = $rg_auto_name #else #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) @@ -140,15 +141,17 @@ #set $use_rg = str($rg.rg_selector) != "do_not_set" </token> <xml name="read_group_auto_name_conditional"> - <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" /> - <when value="true"> - </when> - <when value="false"> + <param name="do_auto_name" type="select" optional="false" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"/> + <when value="no"> <yield /> </when> </xml> <xml name="read_group_id_param"> - <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> + <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment"> <validator type="empty_field" /> </param> </xml> @@ -173,7 +176,7 @@ as per Picard. --> <xml name="read_group_sm_param_required"> - <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> + <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced"> <validator type="empty_field" /> </param> </xml> @@ -196,7 +199,7 @@ </param> </xml> <xml name="read_group_lb_param"> - <param name="LB" type="text" label="Library name (LB)" optional="true" /> + <param name="LB" type="text" label="Library name (LB)"/> </xml> <xml name="read_group_lb_conditional"> <conditional name="read_group_lb_conditional"> @@ -206,7 +209,7 @@ </conditional> </xml> <xml name="read_group_lb_required_param"> - <param name="LB" type="text" label="Library name (LB)" optional="false"> + <param name="LB" type="text" label="Library name (LB)"> <validator type="empty_field" /> </param> </xml> @@ -227,8 +230,8 @@ <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> </xml> <xml name="read_group_fo_param"> - <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> - <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> + <param name="FO" type="text" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> + <validator type="regex" message="Invalid flow order">|\*|[ACMGRSVTWYHKDBN]+$</validator> </param> </xml> <xml name="read_group_ks_param"> @@ -241,10 +244,10 @@ <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> </xml> <xml name="read_group_pu_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> + <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" /> </xml> <xml name="read_group_pu_required_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec"> @@ -287,10 +290,8 @@ <when value="set"> <expand macro="read_group_inputs_spec" /> </when> - <when value="set_id_auto"> - </when> - <when value="do_not_set"> - </when> + <when value="set_id_auto"/> + <when value="do_not_set"/> </conditional> </xml> <xml name="paired_end_options">