Mercurial > repos > iuc > stacks2_cstacks
diff macros_process.xml @ 2:fcce77c09289 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Thu, 16 Jul 2020 07:23:04 -0400 |
| parents | f4aab9196d1e |
| children | 0cd2df8af811 |
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--- a/macros_process.xml Mon Sep 30 14:18:15 2019 -0400 +++ b/macros_process.xml Thu Jul 16 07:23:04 2020 -0400 @@ -29,12 +29,12 @@ <xml name="discover_faqgz_output_macro" token_pattern="" token_dir=""> <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/> - <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" /> - <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" /> + <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/"/> + <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/"/> </xml> <xml name="discover_faq_output_macro" token_pattern="" token_dir=""> - <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" /> - <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" /> + <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/> + <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/> </xml> <xml name="process_outputs"> @@ -71,17 +71,17 @@ <option value="no" selected="true">No</option> </param> <when value="yes"> - <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" /> - <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" /> - <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> + <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1"/> + <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded"/> + <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/> <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> - <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" /> + <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/> </when> <when value="no"> <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/> </when> </conditional> - <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> + <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/> </xml> <token name="@PROCESS_FILTER@"><![CDATA[ #if $filter_cond.filter_select == 'yes': @@ -104,30 +104,30 @@ ## fix the _R[12]_0 that was added for preparing the input #if $input_type.input_type_select == 'paired': - && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done + && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done) #end if ## also remove the gz which is added by procrad (but its uncompressed) - && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done + && (find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done) ## the discard files are named fastq even if the output is fasta #if str($outype).endswith("fasta"): - && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done + && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done) #else - && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done + && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done) #end if #end if ## prepare paired read output for processing in galaxy #if $input_type.input_type_select == 'paired': && mkdir stacks_outputs/remaining - && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done - && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done + && (find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done) + && (find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done) #end if ]]></token> <!-- adapter trimming options --> <xml name="process_adapter"> - <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" /> - <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" /> + <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read"/> + <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read"/> <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/> </xml> <token name="@PROCESS_ADAPTER@"><![CDATA[ @@ -171,8 +171,8 @@ <!-- advanced options that are shared --> <xml name="common_advanced"> - <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> - <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" /> + <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value"/> + <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output"/> </xml> <token name="@COMMON_ADVANCED@"><![CDATA[ #if str($options_advanced.truncate) @@ -181,3 +181,4 @@ $options_advanced.retain_header ]]></token> </macros> +