Mercurial > repos > iuc > tn93_readreduce
comparison readreduce.xml @ 0:bdaadfd0c843 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
| author | iuc |
|---|---|
| date | Wed, 17 Jul 2019 13:41:47 -0400 |
| parents | |
| children | 1d2ec0b0a0a7 |
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| -1:000000000000 | 0:bdaadfd0c843 |
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| 1 <tool id="tn93_readreduce" name="Merge matching reads" version="@VERSION@"> | |
| 2 <description>into clusters with TN-93</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="@VERSION@">tn93</requirement> | |
| 8 </requirements> | |
| 9 <version_command><![CDATA[tn93 --version]]></version_command> | |
| 10 <command detect_errors="exit_code"><![CDATA[ | |
| 11 readreduce | |
| 12 -q | |
| 13 -o '$output' | |
| 14 #if str($options.advanced) == 'advanced': | |
| 15 -a $options.ambigs | |
| 16 -l $options.overlap | |
| 17 #if $options.counts_in_name: | |
| 18 -d '$options.counts_in_name' | |
| 19 #end if | |
| 20 -s '$size' | |
| 21 #end if | |
| 22 '$input' | |
| 23 ]]></command> | |
| 24 <inputs> | |
| 25 <param name="input" type="data" format="fasta" label="Input in FASTA format" /> | |
| 26 <conditional name="options"> | |
| 27 <param label="Additional options" name="advanced" type="select"> | |
| 28 <option value="defaults">Use defaults</option> | |
| 29 <option value="advanced">Specify additional parameters</option> | |
| 30 </param> | |
| 31 <when value="defaults" /> | |
| 32 <when value="advanced"> | |
| 33 <param name="size" argument="-s" type="integer" min="0" value="18" label="Mimimum cluster size to report in output" /> | |
| 34 <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides"> | |
| 35 <option value="handle">handle</option> | |
| 36 <option value="resolve">resolve</option> | |
| 37 <option value="average">average</option> | |
| 38 <option value="skip">skip</option> | |
| 39 <option value="gapmm">gapmm</option> | |
| 40 </param> | |
| 41 <param name="overlap" argument="-l" type="integer" value="100" | |
| 42 label="Only count pairs that overlap by at least N bases" /> | |
| 43 <param name="counts_in_name" argument="-d" type="text" | |
| 44 optional="true" label="Sequence name component immediately preceding a copy number" /> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 </inputs> | |
| 48 <outputs> | |
| 49 <data format="fasta" name="output" /> | |
| 50 </outputs> | |
| 51 <tests> | |
| 52 <test> | |
| 53 <param name="input" value="readreduce-in1.fa" /> | |
| 54 <output file="readreduce-out1.fa" ftype="fasta" name="output" sort="True" /> | |
| 55 </test> | |
| 56 <test> | |
| 57 <param name="input" value="readreduce-in2.fa" /> | |
| 58 <output file="readreduce-out2.fa" ftype="fasta" name="output" sort="True" /> | |
| 59 </test> | |
| 60 </tests> | |
| 61 <help>< algorithm. | |
| 67 ]]></help> | |
| 68 <expand macro="citations" /> | |
| 69 </tool> |