Mercurial > repos > matthias > stacks2_tsv2bam
changeset 6:2626e58c493e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
| author | matthias |
|---|---|
| date | Tue, 25 Jun 2019 10:58:48 -0400 |
| parents | 852044374da1 |
| children | |
| files | macros.xml stacks_tsv2bam.xml test-data/.gentest.sh.swp |
| diffstat | 3 files changed, 10 insertions(+), 6 deletions(-) [+] |
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--- a/macros.xml Thu Jun 20 08:13:59 2019 -0400 +++ b/macros.xml Tue Jun 25 10:58:48 2019 -0400 @@ -107,12 +107,12 @@ <!-- log file handling --> <token name="@TEE_APPEND_LOG@"><![CDATA[ #if $output_log - 2>> $output_log && + 2>> '$output_log' && #end if ]]></token> <token name="@CAT_LOG_TO_STDERR@"><![CDATA[ #if $output_log - cat $output_log 2>&1 + cat '$output_log' 2>&1 #end if ]]></token> <xml name="in_log"> @@ -216,11 +216,15 @@ </expand> </xml> - <!-- fastq input (used in denovomap, tsv2bam, ustacks) --> - <xml name="fastq_input" token_fastq_optional="false" token_help=""> + <!-- fastq input (used in denovomap, tsv2bam, ustacks) + - fastq_optional: makes fastq input optional (true/false) + - se_option: wording for "single end" option (for tsv2bam this is the + reverse reads for the others its the forward reads) + - help: help text --> + <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help=""> <conditional name="input_type"> <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@"> - <option value="single" selected="true">single end or forward reads</option> + <option value="single" selected="true">@SE_OPTION@</option> <option value="paired">(paired) dataset list</option> </param> <when value="single">
--- a/stacks_tsv2bam.xml Thu Jun 20 08:13:59 2019 -0400 +++ b/stacks_tsv2bam.xml Tue Jun 25 10:58:48 2019 -0400 @@ -54,7 +54,7 @@ <expand macro="input_cat_macro"/> <expand macro="input_matches_macro"/> <!-- TODO add BAM? --> - <expand macro="fastq_input" fastq_optional="true" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam"/> + <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/> <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> <expand macro="in_log"/> </inputs>