Mercurial > repos > okorol > itsx

comparison ITSx.xml @ 5:c711ca9a7f4c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author okorol
date Fri, 05 Jun 2015 11:10:49 -0400
parents 2986d8c4db11
children 8a6312fa4633
comparison
equal deleted inserted replaced
4:2986d8c4db11 5:c711ca9a7f4c
3 <description> 3 <description>
4 ITSx -- Identifies ITS sequences and extracts the ITS region 4 ITSx -- Identifies ITS sequences and extracts the ITS region
5 </description> 5 </description>
6 6
7 <command interpreter="perl"> 7 <command interpreter="perl">
8 ITSx -i $input --detailed_results T --cpu $cpu $preserve $reset 8 ITSx -i $input --detailed_results T -N $domain_num --cpu ${NSLOTS} $preserve $reset
9 </command> 9 </command>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="3.1b1">hmmer</requirement> 11 <requirement type="package" version="3.1b1">hmmer</requirement>
12 </requirements> 12 </requirements>
13 <inputs> 13 <inputs>
14 <param name="input" type="data" format="fasta" label="Input Fasta"/> 14 <param name="input" type="data" format="fasta" label="Input Fasta"/>
15 <param name="cpu" type="integer" value="1" label="cpu"/> 15 <param name="domain_num" type="integer" value="2" label="Minimum number of domains"
16 help="The minimum number of domains (different HMM gene profiles) that must match a sequence or it to be included in the output (detected as an ITS sequence). Setting the value lower than two will increase the number of false positives, while increasing it above two will decrease ITSx detection abilities on fragmentary data. "/>
17 <!-- <param name="cpu" type="integer" value="1" label="cpu"/> -->
16 <param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Check both DNA strands against the database"/> 18 <param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Check both DNA strands against the database"/>
17 <param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/> 19 <param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/>
18 <param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/> 20 <param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/>
19 <param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/> 21 <param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/>
20 </inputs> 22 </inputs>