Mercurial > repos > iuc > stacks_denovomap
comparison stacks_denovomap.xml @ 4:998dfec32bde draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
| author | iuc |
|---|---|
| date | Mon, 26 Sep 2016 11:44:20 -0400 |
| parents | bab631cc9f64 |
| children | 34000c653ae5 |
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| 3:bab631cc9f64 | 4:998dfec32bde |
|---|---|
| 1 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.1"> | 1 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0"> |
| 2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description> | 2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 125 #if str($assembly_options.N): | 125 #if str($assembly_options.N): |
| 126 -N $assembly_options.N | 126 -N $assembly_options.N |
| 127 #end if | 127 #end if |
| 128 -M $assembly_options.M | 128 -M $assembly_options.M |
| 129 -n $assembly_options.n | 129 -n $assembly_options.n |
| 130 -t $assembly_options.t | 130 $assembly_options.t |
| 131 -H $assembly_options.H | 131 $assembly_options.H |
| 132 | 132 |
| 133 ## Batch description | 133 ## Batch description |
| 134 -b 1 | 134 -b 1 |
| 135 | 135 |
| 136 ## No SQL recording | 136 ## No SQL recording |
| 177 <section name="assembly_options" title="Assembly options" expanded="false"> | 177 <section name="assembly_options" title="Assembly options" expanded="false"> |
| 178 <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" /> | 178 <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" /> |
| 179 <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" /> | 179 <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" /> |
| 180 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/> | 180 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/> |
| 181 <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" /> | 181 <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" /> |
| 182 <param name="n" argument="-n" type="integer" value="1" label="specify the number of mismatches allowed between loci when building the catalog"/> | 182 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/> |
| 183 | 183 |
| 184 <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" /> | 184 <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" /> |
| 185 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> | 185 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> |
| 186 </section> | 186 </section> |
| 187 | 187 |
| 529 @STACKS_INFOS@ | 529 @STACKS_INFOS@ |
| 530 ]]> | 530 ]]> |
| 531 </help> | 531 </help> |
| 532 <expand macro="citation" /> | 532 <expand macro="citation" /> |
| 533 </tool> | 533 </tool> |
| 534 |