Mercurial > repos > drosofff > msp_oases

comparison oases_optimiser.xml @ 3:f08d9c814ffb draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit b633128427cd321afbe66aa14098a72038068e73
author drosofff
date Tue, 29 Sep 2015 06:29:42 -0400
parents b5df930313cc
children dc684e37f668
comparison
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2:b5df930313cc 3:f08d9c814ffb
1 <tool id="oasesoptimiserv" name="Oases_optimiser" version="1.1.3"> 1 <tool id="oasesoptimiserv" name="Oases_optimiser" version="1.1.4">
2 <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description> 2 <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.08_7a32460a60929b510037952ae815bb6e29b68123">oases</requirement> 4 <requirement type="package" version="0.2.08_7a32460a60929b510037952ae815bb6e29b68123">oases</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 oases_optimiser.py '$start_hash_length' '$end_hash_length' 7 oases_optimiser.py '$start_hash_length' '$end_hash_length'
8 '#for $i in $inputs 8 '#for $i in $inputs
9 ${i.input} 9 ${i.input}
10 #end for 10 #end for
11 ' 11 '
12 '$transcripts' 12 '$transcripts'
13 </command> 13 </command>
14 14
15 <inputs> 15 <inputs>
16 <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems."> 16 <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems.">
20 <option value="17">17</option> 20 <option value="17">17</option>
21 <option value="19">19</option> 21 <option value="19">19</option>
22 <option value="21">21</option> 22 <option value="21">21</option>
23 <option value="23">23</option> 23 <option value="23">23</option>
24 <option value="25">25</option> 24 <option value="25">25</option>
25 25 <option value="35">35</option>
26 <option value="45">45</option>
27 <option value="55">55</option>
28 <option value="65">65</option>
26 </param> 29 </param>
27 <param label="End Hash Length" name="end_hash_length" type="select" help="k-mer length in base pairs of the words being hashed."> 30 <param label="End Hash Length" name="end_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Value has to be higher than the Start Hash Length value">
28 <option value="25">25</option> 31 <option value="25">25</option>
29 <option value="27">27</option> 32 <option value="27">27</option>
30 <option value="29">29</option> 33 <option value="29">29</option>
31 <option value="31">31</option> 34 <option value="31">31</option>
32 <option value="33">33</option> 35 <option value="33">33</option>
33 <option value="35">35</option> 36 <option value="35">35</option>
37 <option value="45">45</option>
38 <option value="55">55</option>
39 <option value="63">63</option>
40 <option value="69">69</option>
34 </param> 41 </param>
35 42
36 43
37 44
38 <repeat name="inputs" title="Input Files"> 45 <repeat name="inputs" title="Input Files">