Mercurial > repos > mvdbeek > generate_sliding_windows

comparison generate_sliding_windows.xml @ 5:79e43a3b0883 draft default tip

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author mvdbeek
date Wed, 15 Apr 2015 10:14:04 -0400
parents cb2d94bb6772
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4:cb2d94bb6772 5:79e43a3b0883
1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.3"> 1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.2.0">
2 <description>Split fasta sequence in nucleotide windows</description> 2 <description>Split fasta sequence in nucleotide windows</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.65">biopython</requirement> 4 <requirement type="package" version="1.65">biopython</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 9
10 <command interpreter="python"><![CDATA[ 10 <command interpreter="python"><![CDATA[
11 generate_sliding_windows.py --input "$input" --output "$output" --window $window --step $step 11 generate_sliding_windows.py --input
12 #if $refFastaSource.fastaSource == "history":
13 "$input"
14 #else
15 "$refFastaSource.pre_installed_fasta.fields.path"
16 #end if
17 --output "$output" --window $window --step $step
12 ]]></command> 18 ]]></command>
13 <inputs> 19 <inputs>
14 <conditional name="refFastaSource"> 20 <conditional name="refFastaSource">
15 <param help="" label="Will you select a fasta sequence from your history or use a pre-installed sequence?" name="fastaSource" type="select"> 21 <param help="" label="Will you select a fasta sequence from your history or use a pre-installed sequence?" name="fastaSource" type="select">
16 <option value="history">Use one from the history</option> 22 <option value="history">Use one from the history</option>
17 <option value="pre-installed">Use a pre-installed fasta sequence</option> 23 <option value="pre_installed">Use a pre-installed fasta sequence</option>
18 </param> 24 </param>
19 <when value="pre-installed"> 25 <when value="pre_installed">
20 <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="input" type="select"> 26 <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="pre_installed_fasta" type="select">
21 <options from_data_table="all_fasta"> 27 <options from_data_table="all_fasta">
22 </options> 28 </options>
23 </param> 29 </param>
24 </when> 30 </when>
25 <when value="history"> 31 <when value="history">