Mercurial > repos > devteam > fasta_compute_length

comparison fasta_compute_length.xml @ 3:2051602a5f97 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
author devteam
date Wed, 11 Sep 2019 09:41:59 -0400
parents de2db1bdfbf8
children e12f68d2cc4e
comparison
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2:de2db1bdfbf8 3:2051602a5f97
1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.1"> 1 <?xml version="1.0"?>
2 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.2">
2 <description></description> 3 <description></description>
3 <command interpreter="python">fasta_compute_length.py $input $output $keep_first $keep_first_word</command> 4 <command>
5 #if $ref.ref_source == 'dbkey':
6 cp '${ref.index.fields.len_path}' '$output'
7 #else:
8 python $__tool_directory__/fasta_compute_length.py
9 #if $ref.ref_source == 'history':
10 '$input'
11 #else:
12 '${ref.index.fields.path}'
13 #end if
14 '$output'
15 $ref.keep_first
16 $ref.keep_first_word
17 #end if
18 </command>
4 <inputs> 19 <inputs>
5 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/> 20 <conditional name="ref">
6 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/> 21 <param name="ref_source" type="select" label="Sequences">
7 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc" 22 <option value="history" selected="True">From History</option>
8 selected="false" label="Strip fasta description from header?" 23 <option value="dbkey">Locally Cached (pre-built length files)</option>
9 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/> 24 <option value="fasta">Locally Cached (full genomes)</option>
25 </param>
26 <when value="history">
27 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
28 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
29 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
30 label="Strip fasta description from header?"
31 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
32 </when>
33 <when value="dbkey">
34 <param name="index" type="select" label="Source Genome Build">
35 <options from_data_table="__dbkeys__"/>
36 </param>
37 </when>
38 <when value="fasta">
39 <param name="index" type="select" label="Source Genome Build">
40 <options from_data_table="all_fasta"/>
41 </param>
42 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
43 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
44 label="Strip fasta description from header?"
45 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
46 </when>
47 </conditional>
10 48
11 </inputs> 49 </inputs>
12 <outputs> 50 <outputs>
13 <data name="output" format="tabular"/> 51 <data name="output" format="tabular"/>
14 </outputs> 52 </outputs>
15 <tests> 53 <tests>
16 <test> 54 <test>
17 <param name="input" value="454.fasta" /> 55 <param name="ref|input" value="454.fasta" />
18 <param name="keep_first" value="0"/> 56 <param name="ref|keep_first" value="0"/>
19 <param name="keep_first_word" value="id_and_desc" /> 57 <param name="ref|keep_first_word" value="id_and_desc" />
20 <output name="output" file="fasta_tool_compute_length_1.out" /> 58 <output name="output" file="fasta_tool_compute_length_1.out" />
21 </test> 59 </test>
22 60
23 <test> 61 <test>
24 <param name="input" value="extract_genomic_dna_out1.fasta" /> 62 <param name="ref|input" value="extract_genomic_dna_out1.fasta" />
25 <param name="keep_first" value="0"/> 63 <param name="ref|keep_first" value="0"/>
26 <param name="keep_first_word" value="id_and_desc" /> 64 <param name="ref|keep_first_word" value="id_and_desc" />
27 <output name="output" file="fasta_tool_compute_length_2.out" /> 65 <output name="output" file="fasta_tool_compute_length_2.out" />
28 </test> 66 </test>
29 67
30 <test> 68 <test>
31 <param name="input" value="454.fasta" /> 69 <param name="ref|input" value="454.fasta" />
32 <param name="keep_first" value="14"/> 70 <param name="ref|keep_first" value="14"/>
33 <param name="keep_first_word" value="id_and_desc" /> 71 <param name="ref|keep_first_word" value="id_and_desc" />
34 <output name="output" file="fasta_tool_compute_length_3.out" /> 72 <output name="output" file="fasta_tool_compute_length_3.out" />
73 </test>
74
75 <test>
76 <param name="ref|ref_source" value="fasta" />
77 <param name="ref|index" value="test_id"/>
78 <param name="ref|keep_first_word" value="id_only" />
79 <output name="output" file="merged.tab" />
80 </test>
81
82 <test>
83 <param name="ref|ref_source" value="dbkey" />
84 <param name="ref|index" value="test_id"/>
85 <output name="output" file="merged.tab" />
35 </test> 86 </test>
36 </tests> 87 </tests>
37 <help> 88 <help>
38 89
39 **What it does** 90 **What it does**