Mercurial > repos > galaxyp > filter_by_fasta_ids
annotate filter_by_fasta_ids.xml @ 5:dff7df6fcab5 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
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date | Wed, 15 May 2019 03:18:11 -0400 |
parents | cd22452edec2 |
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rev | line source |
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5
dff7df6fcab5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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4
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changeset
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1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.3"> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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2 <description>on the headers and/or the sequences</description> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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3 <macros> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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4 <xml name="regexp_macro" token_label="Regular expression pattern"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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5 <param name="regexp" type="text" value="" label="@LABEL@" help="Use the Python regular expression syntax as specified in https://docs.python.org/3/library/re.html"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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6 <validator type="empty_field" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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changeset
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7 <sanitizer> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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changeset
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8 <valid initial="string.printable"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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9 <remove value="'"/> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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changeset
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10 </valid> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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11 <mapping initial="none"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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12 <add source="'" target="'"'"'" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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changeset
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13 </mapping> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
1
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changeset
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14 </sanitizer> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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changeset
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15 </param> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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changeset
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16 </xml> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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changeset
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17 </macros> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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changeset
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18 <requirements> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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19 <requirement type="package" version="3.6.5">python</requirement> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
1
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changeset
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20 </requirements> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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21 <command><![CDATA[ |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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22 python '$__tool_directory__/filter_by_fasta_ids.py' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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23 -i '$input' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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24 #if $header_criteria.header_criteria_select == 'id_list' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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25 --id_list '$header_criteria.identifiers' |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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26 #if $header_criteria.id_regex.find == 'pattern': |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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2
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changeset
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27 --pattern '$header_criteria.id_regex.pattern' |
4
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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28 #else: |
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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29 --pattern '>([^| ]+)' |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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30 #end if |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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31 #elif $header_criteria.header_criteria_select == 'regexp' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
1
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32 --header_regexp '$header_criteria.regexp' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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33 #end if |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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34 #if $sequence_criteria.sequence_criteria_select == 'seq_length' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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35 --min_length $sequence_criteria.min_length |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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36 #if str($sequence_criteria.max_length) |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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37 --max_length $sequence_criteria.max_length |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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38 #end if |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
1
diff
changeset
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39 #elif $sequence_criteria.sequence_criteria_select == 'regexp' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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40 --sequence_regexp '$sequence_criteria.regexp' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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41 #end if |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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42 $dedup |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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43 -o '$output' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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44 #if $output_discarded |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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45 -d '$discarded' |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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46 #end if |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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47 ]]></command> |
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8d15aebf55fd
planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30
galaxyp
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48 <inputs> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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49 <param name="input" type="data" format="fasta" label="FASTA sequences"/> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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changeset
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50 <conditional name="header_criteria"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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51 <param name="header_criteria_select" type="select" label="Criteria for filtering on the headers"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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52 <option value="">No filtering</option> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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53 <option value="id_list">List of IDs</option> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
1
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54 <option value="regexp">Regular expression on the headers</option> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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55 </param> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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56 <when value="" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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57 <when value="id_list"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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1
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58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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59 <conditional name="id_regex"> |
4
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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60 <param name="find" type="select" label="Match IDs by" |
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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61 help="Default: >ID will use search pattern >([^| ]+) to input ID; Use custom regex to change"> |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
parents:
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62 <option value="beginning">Default: ID is expected at the beginning: >ID </option> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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63 <option value="pattern">Custom regex pattern</option> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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64 </param> |
4
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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diff
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65 <when value="beginning" /> |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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66 <when value="pattern"> |
4
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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67 <param name="pattern" type="text" value="" label="Regex search pattern for ID" |
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
galaxyp
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68 help="Search pattern must contain %s where the ID will be substituted. Use this for Uniprot Acc: >.+?\|(.+?)\|.*$"> |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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69 <sanitizer sanitize="False"/> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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70 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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71 </param> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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|
72 </when> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
parents:
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changeset
|
73 </conditional> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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changeset
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74 </when> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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75 <when value="regexp"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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76 <expand macro="regexp_macro" label="Regular expression pattern the header should match" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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77 </when> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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78 </conditional> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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changeset
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79 <conditional name="sequence_criteria"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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80 <param name="sequence_criteria_select" type="select" label="Criteria for filtering on the sequences"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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81 <option value="">No filtering</option> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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changeset
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82 <option value="seq_length">Sequence length</option> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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changeset
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83 <option value="regexp">Regular expression on the sequences</option> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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84 </param> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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85 <when value="" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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86 <when value="seq_length"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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87 <param name="min_length" type="integer" value="0" label="Minimum length" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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88 <param name="max_length" type="integer" min="1" value="" optional="true" label="Maximum length" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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89 </when> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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90 <when value="regexp"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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91 <expand macro="regexp_macro" label="Regular expression pattern the sequence should match" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
parents:
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92 </when> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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93 </conditional> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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94 <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" label="Remove duplicate sequences" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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95 <param name="output_discarded" type="boolean" label="Output discarded FASTA entries" /> |
1
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96 </inputs> |
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97 <outputs> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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98 <data name="output" format="fasta" label="${tool.name} on ${on_string}: FASTA sequences"/> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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99 <data name="discarded" format="fasta" label="${tool.name} on ${on_string}: discarded entries"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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100 <filter>output_discarded</filter> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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101 </data> |
1
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102 </outputs> |
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103 <tests> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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104 <test expect_num_outputs="1"> |
1
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105 <param name="input" ftype="fasta" value="input.fasta" /> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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106 <param name="header_criteria_select" value="id_list" /> |
1
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galaxyp
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107 <param name="identifiers" ftype="txt" value="ids.txt" /> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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108 <param name="dedup" value="True" /> |
1
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109 <output name="output" file="output_dedup.fasta" /> |
8d15aebf55fd
planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30
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110 </test> |
3
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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111 <test expect_num_outputs="1"> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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112 <param name="input" ftype="fasta" value="input_sp.fasta" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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113 <param name="header_criteria_select" value="id_list" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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114 <param name="find" value="pattern" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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115 <param name="pattern" value=">.+?\|(.+?)\|.*$" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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116 <param name="identifiers" ftype="txt" value="ids_sp.txt" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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117 <param name="dedup" value="True" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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118 <output name="output" file="output_sp_dedup.fasta" /> |
3c623e81be77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
galaxyp
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119 </test> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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120 <test expect_num_outputs="2"> |
1
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121 <param name="input" ftype="fasta" value="input.fasta" /> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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122 <param name="header_criteria_select" value="id_list" /> |
1
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123 <param name="identifiers" ftype="txt" value="ids.txt" /> |
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124 <param name="dedup" value="False" /> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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125 <param name="output_discarded" value="True" /> |
1
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126 <output name="output" file="output_not_dedup.fasta" /> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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127 <output name="discarded" file="discarded_not_dedup.fasta" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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128 </test> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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129 <test expect_num_outputs="2"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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130 <param name="input" ftype="fasta" value="input.fasta" /> |
4
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
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131 <conditional name="header_criteria"> |
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
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132 <param name="header_criteria_select" value="regexp" /> |
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
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133 <param name="regexp" value="2" /> |
cd22452edec2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
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134 </conditional> |
2
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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135 <param name="dedup" value="False" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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136 <param name="output_discarded" value="True" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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137 <output name="output" file="output_header_regexp.fasta" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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138 <output name="discarded" file="discarded_header_regexp.fasta" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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139 </test> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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140 <test expect_num_outputs="2"> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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141 <param name="input" ftype="fasta" value="input.fasta" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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142 <param name="sequence_criteria_select" value="seq_length" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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143 <param name="min_length" value="5" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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144 <param name="dedup" value="False" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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145 <param name="output_discarded" value="True" /> |
1bd985f14938
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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146 <output name="output" file="output_min_length5.fasta" /> |
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147 <output name="discarded" file="discarded_min_length5.fasta" /> |
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148 </test> |
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149 <test expect_num_outputs="2"> |
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150 <param name="input" ftype="fasta" value="input.fasta" /> |
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151 <param name="sequence_criteria_select" value="seq_length" /> |
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152 <param name="max_length" value="4" /> |
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153 <param name="dedup" value="False" /> |
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154 <param name="output_discarded" value="True" /> |
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155 <output name="output" file="output_max_length4.fasta" /> |
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156 <output name="discarded" file="discarded_max_length4.fasta" /> |
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157 </test> |
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158 <test expect_num_outputs="2"> |
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159 <param name="input" ftype="fasta" value="input.fasta" /> |
4
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160 <conditional name="sequence_criteria"> |
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161 <param name="sequence_criteria_select" value="regexp" /> |
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162 <param name="regexp" value="T{2,}" /> |
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163 </conditional> |
2
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164 <param name="dedup" value="False" /> |
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165 <param name="output_discarded" value="True" /> |
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166 <output name="output" file="output_sequence_regexp.fasta" /> |
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167 <output name="discarded" file="discarded_sequence_regexp.fasta" /> |
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168 </test> |
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169 <test expect_num_outputs="2"> |
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170 <param name="input" ftype="fasta" value="input.fasta" /> |
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171 <conditional name="header_criteria"> |
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172 <param name="header_criteria_select" value="regexp" /> |
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173 <param name="regexp" value="3|5" /> |
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174 </conditional> |
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175 <conditional name="sequence_criteria"> |
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176 <param name="sequence_criteria_select" value="regexp" /> |
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177 <param name="regexp" value="ACGT" /> |
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178 </conditional> |
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179 <param name="dedup" value="False" /> |
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180 <param name="output_discarded" value="True" /> |
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181 <output name="output" file="output_header_regexp_sequence_regexp.fasta" /> |
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182 <output name="discarded" file="discarded_header_regexp_sequence_regexp.fasta" /> |
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183 </test> |
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184 </tests> |
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185 <help><![CDATA[ |
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186 **What it does** |
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187 |
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188 Filter entries of a FASTA file on the headers and/or the sequences based on various criteria. |
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189 ]]></help> |
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190 </tool> |