Mercurial > repos > cpt > cpt_putative_isp
comparison generate-putative-isp.xml @ 5:0f6659efd912 draft
planemo upload commit d213efcbada7995b34f93ed64202e551fa4fcf07
author | cpt |
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date | Wed, 18 Sep 2024 04:44:36 +0000 |
parents | bc16792ecfd2 |
children | 7a0ed74e9ff8 |
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4:bc16792ecfd2 | 5:0f6659efd912 |
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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> |