comparison generate-putative-isp.xml @ 5:0f6659efd912 draft

planemo upload commit d213efcbada7995b34f93ed64202e551fa4fcf07
author cpt
date Wed, 18 Sep 2024 04:44:36 +0000
parents bc16792ecfd2
children 7a0ed74e9ff8
comparison
equal deleted inserted replaced
4:bc16792ecfd2 5:0f6659efd912
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="2019.06.08">regex</requirement> 7 <requirement type="package" version="2019.06.08">regex</requirement>
8 <requirement type="package" version="1.77">biopython</requirement>
8 </expand> 9 </expand>
9 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
10 python '$__tool_directory__/generate-putative-isp.py' 11 python '$__tool_directory__/generate-putative-isp.py'
11 '$fasta_file' 12 '$fasta_file'
12 --strand '$strand' 13 --strand '$strand'
13 --switch '$switch' 14 --switch '$switch'
14 --isp_on '$isp_on' 15 --isp_on '$isp_on'
15 --isp_op '$isp_op' 16 --isp_op '$isp_op'
16 --isp_ob '$isp_ob' 17 --isp_ob '$isp_ob'
17 --isp_og '$isp_og' 18 --isp_og '$isp_og'
18 --isp_min_len '$isp_min_len' 19 --isp_min_len '$isp_min_len'
19 --isp_min_dist '$isp_min_dist' 20 --isp_min_dist '$isp_min_dist'
20 --isp_max_dist '$isp_max_dist' 21 --isp_max_dist '$isp_max_dist'
21 --min_tmd_size '$min_tmd_size' 22 --min_tmd_size '$min_tmd_size'
22 --max_tmd_size '$max_tmd_size' 23 --max_tmd_size '$max_tmd_size'
23 --putative_isp '$putative_isp' 24 --putative_isp '$putative_isp'
24 --summary_isp_txt '$summary_isp' 25 --summary_isp_txt '$summary_isp'
25 --putative_isp_gff '$putative_isp_gff' 26 --putative_isp_gff '$putative_isp_gff'
26 --isp_max '$isp_max' 27 --isp_max '$isp_max'
27 --peri_min '$peri_min' 28 --peri_min '$peri_min'
28 --peri_max '$peri_max' 29 --peri_max '$peri_max'
29 30 ]]></command>
30 ]]></command>
31 <inputs> 31 <inputs>
32 <param type="select" label="Strand Choice" name="strand"> 32 <param type="select" label="Strand Choice" name="strand">
33 <option value="both">both</option> 33 <option value="both">both</option>
34 <option value="forward">+</option> 34 <option value="forward">+</option>
35 <option value="reverse">-</option> 35 <option value="reverse">-</option>