Mercurial > repos > iuc > stacks_procrad
comparison stacks_procrad.xml @ 12:eded025438db draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 22:00:56 +0000 |
| parents | be78e39d56b3 |
| children |
comparison
equal
deleted
inserted
replaced
| 11:be78e39d56b3 | 12:eded025438db |
|---|---|
| 1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0"> | 1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0"> |
| 2 <description>the Stacks demultiplexing script</description> | 2 <description>the Stacks demultiplexing script</description> |
| 3 <expand macro="bio_tools"/> | |
| 4 <macros> | 3 <macros> |
| 5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 6 </macros> | 5 </macros> |
| 6 <expand macro="bio_tools"/> | |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 | 10 |
| 11 #if $input_type.options_type_selector == "single" | 11 #if $input_type.options_type_selector == "single" |
| 133 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> | 133 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> |
| 134 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> | 134 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> |
| 135 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> | 135 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> |
| 136 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> | 136 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> |
| 137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> | 137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> |
| 138 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> | 138 <param type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> |
| 139 </section> | 139 </section> |
| 140 | 140 |
| 141 <param name="outype" argument="-y" type="select" label="Output format" > | 141 <param name="outype" argument="-y" type="select" label="Output format" > |
| 142 <option value="auto" selected="True">Same as input</option> | 142 <option value="auto" selected="True">Same as input</option> |
| 143 <option value="fastq">fastq</option> | 143 <option value="fastq">fastq</option> |