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comparison tools/protein_analysis/wolf_psort.xml @ 20:a19b3ded8f33 draft

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v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
author peterjc
date Thu, 21 Sep 2017 11:35:20 -0400
parents eb6ac44d4b8e
children 238eae32483c
comparison
equal deleted inserted replaced
19:f3ecd80850e2 20:a19b3ded8f33
1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.9"> 1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.11">
2 <description>Eukaryote protein subcellular localization prediction</description> 2 <description>Eukaryote protein subcellular localization prediction</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">runWolfPsortSummary</requirement> 4 <requirement type="package">wolfpsort</requirement>
5 <requirement type="binary">psort</requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <version_command>
8 <!-- Anything other than zero is an error --> 7 python $__tool_directory__/wolf_psort.py --version
9 <exit_code range="1:" /> 8 </version_command>
10 <exit_code range=":-1" /> 9 <command detect_errors="aggressive">
11 </stdio> 10 python $__tool_directory__/wolf_psort.py $organism "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
12 <command interpreter="python">
13 wolf_psort.py $organism "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file"
14 ##If the environment variable isn't set, get "", and python wrapper
15 ##defaults to four threads.
16 </command> 11 </command>
17 <inputs> 12 <inputs>
18 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 13 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
19 <param name="organism" type="select" display="radio" label="Organism"> 14 <param name="organism" type="select" display="radio" label="Organism">
20 <option value="animal">Animal</option> 15 <option value="animal">Animal</option>
21 <option value="plant">Plant</option> 16 <option value="plant">Plant</option>
22 <option value="fungi">Fungi</option> 17 <option value="fungi">Fungi</option>
23 </param> 18 </param>
46 <param name="organism" value="fungi"/> 41 <param name="organism" value="fungi"/>
47 <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> 42 <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/>
48 </test> 43 </test>
49 </tests> 44 </tests>
50 <help> 45 <help>
51 46
52 **What it does** 47 **What it does**
53 48
54 This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization. 49 This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization.
55 50
56 The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein): 51 The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein):
76 cyto cytosol 0005829 71 cyto cytosol 0005829
77 cysk cytoskeleton 0005856(2) 72 cysk cytoskeleton 0005856(2)
78 E.R. endoplasmic reticulum 0005783 73 E.R. endoplasmic reticulum 0005783
79 extr extracellular 0005576, 0005618 74 extr extracellular 0005576, 0005618
80 golg Golgi apparatus 0005794(1) 75 golg Golgi apparatus 0005794(1)
81 lyso lysosome 0005764 76 lyso lysosome 0005764
82 mito mitochondria 0005739 77 mito mitochondria 0005739
83 nucl nuclear 0005634 78 nucl nuclear 0005634
84 pero peroxisome 0005777(2) 79 pero peroxisome 0005777(2)
85 plas plasma membrane 0005886 80 plas plasma membrane 0005886
86 vacu vacuolar membrane 0005774(2) 81 vacu vacuolar membrane 0005774(2)
87 ====== ===================== ===================== 82 ====== ===================== =====================
88 83
89 Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of" 84 Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of"
90 cellular components were also included, up to the specified depth (2 in this case). 85 cellular components were also included, up to the specified depth (2 in this case).
91 For example, all of the children and grandchildren of "GO:0005856" were 86 For example, all of the children and grandchildren of "GO:0005856" were
92 included as "cysk". 87 included as "cysk".
93 88
94 Additionally compound predictions like mito_nucl are also given. 89 Additionally compound predictions like mito_nucl are also given.
95 90
96 91
97 **Notes** 92 **Notes**