Mercurial > repos > galaxyp > fasta_merge_files_and_filter_unique_sequences
annotate fasta_merge_files_and_filter_unique_sequences.xml @ 4:8462a4e9f86e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
author | galaxyp |
---|---|
date | Mon, 24 Jul 2017 17:13:10 -0400 |
parents | 9ad0d336e5ed |
children | 650d553c1fda |
rev | line source |
---|---|
4
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
1 <tool id="fasta_merge_files_and_filter_unique_sequences" name="FASTA Merge Files and Filter Unique Sequences" version="1.2.0"> |
1
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
2 <description>Concatenate FASTA database files together</description> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
3 <requirements> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
4 <requirement type="package" version="2.7.12">python</requirement> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
5 </requirements> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
6 <command> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
7 python '$__tool_directory__/fasta_merge_files_and_filter_unique_sequences.py' |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
8 '$output' $uniqueness_criterion '$accession_parser' |
4
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
9 |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
10 #if $batchmode.processmode == 'merge': |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
11 #set $inputs = $batchmode.input_fastas |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
12 #else: |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
13 #set $inputs = [ $batchmode.input_fastas ] |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
14 #end if |
1
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
15 #for $input in $inputs: |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
16 '$input' |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
17 #end for |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
18 </command> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
19 <inputs> |
4
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
20 <conditional name="batchmode"> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
21 <param name="processmode" type="select" label="Run in batch mode?" help="The 'merge all' mode produces one output FASTA for all input FASTA files. The individual mode generates one FASTA file for each set of input FASTAs. For example, if the tool is given 2 collections of 10 FASTAs, it will merge the collections pairwise to create an output collection of 10 FASTAs." display="radio"> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
22 <option value="individual" selected="True">Merge individual FASTAs (output collection if input is collection)</option> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
23 <option value="merge">Merge all FASTAs (always output a single FASTA)</option> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
24 </param> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
25 <when value="individual"> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
26 <param name="input_fastas" type="data" format="fasta" label="FASTA file" /> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
27 </when> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
28 <when value="merge"> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
29 <param name="input_fastas" type="data" format="fasta" multiple="True" label="FASTA file" /> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
30 </when> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
31 </conditional> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
32 <param name="uniqueness_criterion" type="select" label="How are sequences judged to be unique?"> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
33 <option value="sequence" selected="true">Accession and Sequence</option> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
34 <option value="accession">Accession Only</option> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
35 </param> |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
36 <param name="accession_parser" type="text" label="Accession Parsing Regex" value="^>([^ ]+).*$" help="Regular expression with 1 capture group; the capture group is the accession (which must be unique)"> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
37 <sanitizer> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
38 <valid> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
39 <add preset="string.printable"/> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
40 <remove value="\" /> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
41 <remove value="'" /> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
42 </valid> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
43 <mapping initial="none"> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
44 <add source="\" target="__backslash__" /> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
45 <add source="'" target="__sq__"/> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
46 </mapping> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
47 </sanitizer> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
48 </param> |
1
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
49 </inputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
50 <outputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
51 <data format="fasta" name="output" label="Merged and Filtered FASTA from ${on_string}"/> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
52 </outputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
53 <tests> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
54 <test> |
4
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
55 <param name="input_fastas" value="1.fa,2.fa" ftype="fasta" /> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
56 <param name="processmode" value="merge" /> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
57 <param name="uniqueness_criterion" value="sequence" /> |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
58 <param name="accession_parser" value="^>([^ |]+).*$" /> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
59 <output name="output" file="res-sequence.fa" ftype="fasta" /> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
60 <assert_stdout> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
61 <has_line line="Skipping protein '>one_2' with duplicate sequence (first seen as '>one')" /> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
62 <has_line line="Skipping protein '>two_2' with duplicate sequence (first seen as '>two')" /> |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
63 <has_line line="Skipping protein '>three_2|456' with duplicate accession" /> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
64 <has_line line="Skipping protein '>three_2 789' with duplicate accession" /> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
65 </assert_stdout> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
66 </test> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
67 <test> |
4
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
68 <param name="input_fastas" value="1.fa,2.fa" ftype="fasta" /> |
8462a4e9f86e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit b4c90f4b5d7e9b233f1150dbc9e5dcbe156809e8
galaxyp
parents:
3
diff
changeset
|
69 <param name="processmode" value="merge" /> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
70 <param name="uniqueness_criterion" value="accession" /> |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
71 <param name="accession_parser" value="^>([^ |]+).*$" /> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
72 <output name="output" file="res-accession.fa" ftype="fasta" /> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
73 <assert_stdout> |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
74 <has_line line="Skipping protein '>three_2|456' with duplicate accession" /> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
75 <has_line line="Skipping protein '>three_2 789' with duplicate accession" /> |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
76 </assert_stdout> |
1
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
77 </test> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
78 </tests> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
79 <help> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
80 <![CDATA[ |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
81 **What it does** |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
82 |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
83 Concatenate FASTA database files together. |
2
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
84 |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
85 If the uniqueness criterion is "Accession and Sequence", only the first appearence of each unique sequence will appear in the output. |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
86 Otherwise, duplicate sequences are allowed, but only the first appearance of each accession will appear in the output. |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
galaxyp
parents:
1
diff
changeset
|
87 |
3
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
galaxyp
parents:
2
diff
changeset
|
88 The default accession parser will treat everything in the header before the first space as the accession. |
1
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
89 |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
90 ------ |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
91 |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
92 **Citation** |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
93 |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
94 If you use this tool in Galaxy, please the GalaxyP developers at: https://github.com/galaxyproteomics/ |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
95 |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
96 ]]> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
galaxyp
parents:
0
diff
changeset
|
97 </help> |
0 | 98 </tool> |