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comparison generate-putative-isp.xml @ 7:f0ca7edbe202 draft

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planemo upload commit ad5355b899dc8f8300c206522e2a65d49809fb73
author cpt
date Fri, 20 Sep 2024 02:35:30 +0000
parents 7a0ed74e9ff8
children b5c1b167df3c
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6:7a0ed74e9ff8 7:f0ca7edbe202
1 <tool id="edu.tamu.cpt2.spanin.generate-putative-isp" name="ISP candidates" version="1.0"> 1 <tool id="edu.tamu.cpt2.spanin.generate-putative-isp" name="ISP candidates" version="1.0">
2 <description>constructs a putative list of potential i-spanin from an input genomic FASTA</description> 2 <description>constructs a putative list of potential i-spanin from an input genomic FASTA</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements">
7 <requirement type="package" version="3.9">python</requirement>
8 <requirement type="package" version="2019.06.08">regex</requirement> 7 <requirement type="package" version="2019.06.08">regex</requirement>
9 <requirement type="package" version="1.77">biopython</requirement> 8 </expand>
10 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
11 </requirements>
12 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
13 python '$__tool_directory__/generate-putative-isp.py' 10 python '$__tool_directory__/generate-putative-isp.py'
14 '$fasta_file' 11 '$fasta_file'
15 --strand '$strand' 12 --strand '$strand'
16 --switch '$switch' 13 --switch '$switch'
17 --isp_on '$isp_on' 14 --isp_on '$isp_on'
18 --isp_op '$isp_op' 15 --isp_op '$isp_op'
19 --isp_ob '$isp_ob' 16 --isp_ob '$isp_ob'
20 --isp_og '$isp_og' 17 --isp_og '$isp_og'
21 --isp_min_len '$isp_min_len' 18 --isp_min_len '$isp_min_len'
22 --isp_min_dist '$isp_min_dist' 19 --isp_min_dist '$isp_min_dist'
23 --isp_max_dist '$isp_max_dist' 20 --isp_max_dist '$isp_max_dist'
24 --min_tmd_size '$min_tmd_size' 21 --min_tmd_size '$min_tmd_size'
25 --max_tmd_size '$max_tmd_size' 22 --max_tmd_size '$max_tmd_size'
26 --putative_isp '$putative_isp' 23 --putative_isp '$putative_isp'
27 --summary_isp_txt '$summary_isp' 24 --summary_isp_txt '$summary_isp'
28 --putative_isp_gff '$putative_isp_gff' 25 --putative_isp_gff '$putative_isp_gff'
29 --isp_max '$isp_max' 26 --isp_max '$isp_max'
30 --peri_min '$peri_min' 27 --peri_min '$peri_min'
31 --peri_max '$peri_max' 28 --peri_max '$peri_max'
32 ]]></command> 29
30 ]]></command>
33 <inputs> 31 <inputs>
34 <param type="select" label="Strand Choice" name="strand"> 32 <param type="select" label="Strand Choice" name="strand">
35 <option value="both">both</option> 33 <option value="both">both</option>
36 <option value="forward">+</option> 34 <option value="forward">+</option>
37 <option value="reverse">-</option> 35 <option value="reverse">-</option>