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comparison ITSx.xml @ 9:3610c6312b85 draft default tip

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author okorol
date Fri, 05 Jun 2015 12:05:37 -0400
parents 88ea67da0d99
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8:88ea67da0d99 9:3610c6312b85
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 -N $domain_num --cpu=\${NSLOTS:1} $preserve $reset 8 ITSx -i $input --detailed_results T -N $domain_num --cpu=\${GALAXY_SLOTS:-1} $preserve $reset
9 9
10 </command> 10 </command>
11 <requirements> 11 <requirements>
12 <requirement type="package" version="3.1b1">hmmer</requirement> 12 <requirement type="package" version="3.1b1">hmmer</requirement>
13 </requirements> 13 </requirements>
16 <param name="domain_num" type="integer" value="2" label="Minimum number of domains" 16 <param name="domain_num" type="integer" value="2" label="Minimum number of domains"
17 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 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. "/>
18 <!-- <param name="cpu" type="integer" value="1" label="cpu"/> --> 18 <!-- <param name="cpu" type="integer" value="1" label="cpu"/> -->
19 <param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Check both DNA strands against the database"/> 19 <param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Check both DNA strands against the database"/>
20 <param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/> 20 <param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/>
21 <param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/> 21 <param name="reset" type="boolean" checked="true" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/>
22 <param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/> 22 <param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/>
23 </inputs> 23 </inputs>
24 24
25 <outputs> 25 <outputs>
26 <data name="ITS1" format="fasta" label="Extracted ITS1 Fasta File" from_work_dir="ITSx_out.ITS1.fasta"/> 26 <data name="ITS1" format="fasta" label="Extracted ITS1 Fasta File" from_work_dir="ITSx_out.ITS1.fasta"/>