Mercurial > repos > peterjc > fasta_filter_by_id

annotate tools/fasta_filter_by_id/fasta_filter_by_id.xml @ 3:812383b5d3b8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
author peterjc
date Fri, 03 Feb 2017 05:32:34 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
1 <tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.5" hidden="true">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
2 <description>from a tabular file</description>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
3 <requirements>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
5 </requirements>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
6 <version_command interpreter="python">fasta_filter_by_id.py --version</version_command>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
7 <command interpreter="python">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
8 fasta_filter_by_id.py $input_tabular $columns $input_fasta
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
9 #if $output_choice_cond.output_choice=="both"
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
10 $output_pos $output_neg
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
11 #elif $output_choice_cond.output_choice=="pos"
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
12 $output_pos -
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
13 #elif $output_choice_cond.output_choice=="neg"
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
14 - $output_neg
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
15 #end if
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
16 </command>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
17 <inputs>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
18 <param name="input_fasta" type="data" format="fasta" label="FASTA file to filter on the identifiers"/>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
19 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTA identifiers"/>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
20 <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
21 <validator type="no_options" message="Pick at least one column"/>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
22 </param>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
23 <conditional name="output_choice_cond">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
24 <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
25 <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two FASTA files</option>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
26 <option value="pos">Just positive matches (ID on list), as a single FASTA file</option>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
27 <option value="neg">Just negative matches (ID not on list), as a single FASTA file</option>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
28 </param>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
29 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
30 <when value="both" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
31 <when value="pos" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
32 <when value="neg" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
33 </conditional>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
34 </inputs>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
35 <outputs>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
36 <data name="output_pos" format="fasta" label="With matched ID">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
37 <filter>output_choice_cond["output_choice"] != "neg"</filter>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
38 </data>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
39 <data name="output_neg" format="fasta" label="Without matched ID">
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
40 <filter>output_choice_cond["output_choice"] != "pos"</filter>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
41 </data>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
42 </outputs>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
43 <tests>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
44 <test>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
45 <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
46 <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
47 <param name="columns" value="1" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
48 <param name="output_choice" value="both" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
49 <output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
50 <output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
51 </test>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
52 <test>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
53 <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
54 <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
55 <param name="columns" value="1" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
56 <param name="output_choice" value="pos" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
57 <output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
58 </test>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
59 <test>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
60 <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
61 <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
62 <param name="columns" value="1" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
63 <param name="output_choice" value="neg" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
64 <output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" />
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
65 </test>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
66 </tests>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
67 <help>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
68
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
69 **Deprecated**
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
70
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
71 This tool is now obsolete, and should not be used in future. It has been
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
72 replaced by a more general version covering FASTA, FASTQ and SFF in one
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
73 single tool.
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
74
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
75 **What it does**
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
76
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
77 By default it divides a FASTA file in two, those sequences with or without an
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
78 ID present in the tabular file column(s) specified. You can opt to have a
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
79 single output file of just the matching records, or just the non-matching ones.
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
80
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
81 Note that the order of sequences in the original FASTA file is preserved.
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
82 Also, if any sequences share an identifier, duplicates are not removed.
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
83
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
84 **Example Usage**
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
85
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
86 Given a FASTA file of proteins you might run a signal peptide search (e.g.
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
87 via the SignalP wrapper for Galaxy), then filtered these tabular results to
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
88 select just those with a signal peptide. You could then use this tool to get
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
89 a FASTA file of only the proteins with predicted signal peptides.
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
90
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
91 </help>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
92 <citations>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
93 <citation type="doi">10.7717/peerj.167</citation>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
94 </citations>
812383b5d3b8 v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
peterjc
parents:
diff changeset
95 </tool>