Mercurial > repos > galaxyp > fasta_merge_files_and_filter_unique_sequences
annotate fasta_merge_files_and_filter_unique_sequences.xml @ 3:9ad0d336e5ed draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
author | galaxyp |
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date | Fri, 03 Feb 2017 14:27:56 -0500 |
parents | 379c41d859aa |
children | 8462a4e9f86e |
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74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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1 <tool id="fasta_merge_files_and_filter_unique_sequences" name="FASTA Merge Files and Filter Unique Sequences" version="1.1"> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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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
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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
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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
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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
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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
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7 python '$__tool_directory__/fasta_merge_files_and_filter_unique_sequences.py' |
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9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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8 '$output' $uniqueness_criterion '$accession_parser' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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9 #for $input in $inputs: |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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10 '$input' |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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11 #end for |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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12 </command> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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13 <inputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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14 <param name="inputs" format="fasta" multiple="True" type="data" label="Input FASTA files"/> |
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379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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15 <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
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16 <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
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17 <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
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18 </param> |
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9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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19 <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
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20 <sanitizer> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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21 <valid> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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22 <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
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23 <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
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24 <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
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25 </valid> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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26 <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
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27 <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
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28 <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
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29 </mapping> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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30 </sanitizer> |
9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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31 </param> |
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74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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32 </inputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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33 <outputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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34 <data format="fasta" name="output" label="Merged and Filtered FASTA from ${on_string}"/> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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35 </outputs> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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36 <tests> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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37 <test> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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38 <param name="inputs" value="1.fa,2.fa" ftype="fasta" /> |
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379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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39 <param name="uniqueness_criterion" value="sequence" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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40 <param name="accession_parser" value="^>([^ |]+).*$" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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41 <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
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42 <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
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43 <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
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44 <has_line line="Skipping protein '>two_2' with duplicate sequence (first seen as '>two')" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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45 <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
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46 <has_line line="Skipping protein '>three_2 789' with duplicate accession" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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47 </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
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48 </test> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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49 <test> |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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50 <param name="inputs" value="1.fa,2.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
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51 <param name="uniqueness_criterion" value="accession" /> |
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9ad0d336e5ed
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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52 <param name="accession_parser" value="^>([^ |]+).*$" /> |
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379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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53 <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
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54 <assert_stdout> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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55 <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
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56 <has_line line="Skipping protein '>three_2 789' with duplicate accession" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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57 </assert_stdout> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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58 </test> |
74144834b0bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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59 </tests> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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60 <help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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61 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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62 **What it does** |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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63 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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64 Concatenate FASTA database files together. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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65 |
379c41d859aa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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66 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
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67 Otherwise, duplicate sequences are allowed, but only the first appearance of each accession will appear in the output. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f
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68 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 96128b1b32e31c88f08201fd59a07fb1057aafbe
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69 The default accession parser will treat everything in the header before the first space as the accession. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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70 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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71 ------ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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72 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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73 **Citation** |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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74 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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75 If you use this tool in Galaxy, please the GalaxyP developers at: https://github.com/galaxyproteomics/ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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76 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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77 ]]> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
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78 </help> |
0 | 79 </tool> |