Mercurial > repos > mbernt > fasta_regex_finder

annotate fastaregexfinder.xml @ 0:269c627ae9f4 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
author mbernt
date Wed, 20 Jun 2018 11:06:57 -0400
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children 9a811adb714f
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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1 <tool id="fasta_regex_finder" name="fasta_regex_finder" version="0.1.0">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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2 <description>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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3 Search in fasta for regexp match
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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4 </description>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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5 <requirements>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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6 </requirements>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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7 <version_command>python $__tool_directory__/fastaregexfinder.py --version</version_command>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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8 <command detect_errors="exit_code"><![CDATA[
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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9 python $__tool_directory__/fastaregexfinder.py
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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10 --fasta "$input"
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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11 --regex "$regex"
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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12 #if $settings.advanced == "advanced"
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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13 $settings.matchcase
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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14 $settings.noreverse
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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15 --maxstr $settings.maxstr
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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16 #if $settings.seqnames != ""
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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17 --seqnames $settings.seqnames
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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18 #end if
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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19 #end if
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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20 --quiet
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21 > $output
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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22 ]]></command>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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23 <inputs>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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24 <param type="data" name="input" format="fasta" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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25 <param name="regex" size="30" type="text" value="([gG]{3,}\w{1,7}){3,}[gG]{3,}" label="Regular expression" help="(--regex)">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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26 <sanitizer>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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27 <valid initial="string.printable">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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28 <remove value="&apos;"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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29 </valid>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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30 <mapping initial="none">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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31 <add source="&apos;" target="__sq__"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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32 </mapping>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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33 </sanitizer>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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34 </param>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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35 <conditional name="settings">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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36 <param name="advanced" type="select" label="Specify advanced parameters">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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37 <option value="simple" selected="true">No, use program defaults.</option>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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38 <option value="advanced">Yes, see full parameter list.</option>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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39 </param>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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40 <when value="simple">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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41 </when>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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42 <when value="advanced">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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43 <param name="matchcase" type="boolean" label="Match case" truevalue="--matchcase" falsevalue="" help="(--matchcase)" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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44 <param name="noreverse" type="boolean" label="Do not search the reverse complement" truevalue="--noreverse" falsevalue="" help="(--noreverse)" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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45 <param name="maxstr" type="integer" label="Maximum length of the match to report" value="10000" min="1" help="(--maxstr)" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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46 <param name="seqnames" size="30" type="text" value="" label="Space separated list of fasta sequences to search" help="--seqnames"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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47 </when>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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48 </conditional>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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49 </inputs>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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50 <outputs>
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51 <data name="output" format="bed" from_work_dir="TestSeqGroup-G4.bed" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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52 </outputs>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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53 <tests>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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54 <test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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55 <param name="input" value="TestSeqGroup-G4.fasta"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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56 <output name="output" file="TestSeqGroup-G4.bed"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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57 </test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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58 <test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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59 <param name="input" value="test.fas"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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60 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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61 <output name="output" file="test-1.bed"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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62 </test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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63 <test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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64 <param name="input" value="test.fas"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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65 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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66 <param name="advanced" value="advanced"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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67 <param name="matchcase" value="--matchcase"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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68 <output name="output" file="test-2.bed"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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69 </test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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70 <test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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71 <param name="input" value="test.fas"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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72 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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73 <param name="advanced" value="advanced"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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74 <param name="noreverse" value="--noreverse"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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75 <output name="output" file="test-3.bed"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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76 </test>
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77 <test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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78 <param name="input" value="test.fas"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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79 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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80 <param name="advanced" value="advanced"/>
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81 <param name="maxstr" value="3"/>
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82 <output name="output" file="test-4.bed"/>
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83 </test>
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84 <test>
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85 <param name="input" value="TestSeqGroup-G4.fasta"/>
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86 <param name="advanced" value="advanced"/>
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87 <param name="seqnames" value="HJ24-Shp2_oncogenicProtein2 HJ24-Shp2_oncogenicProtein"/>
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88 <output name="output" file="TestSeqGroup-G4-sub.bed"/>
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92 DESCRIPTION
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93
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94 Search a fasta file for matches to a regular expression and return a bed file with the
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95 coordinates of the match and the matched sequence itself.
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96
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97 Output bed file has columns:
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98
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99 1. Name of fasta sequence (e.g. chromosome)
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100 2. Start of the match
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101 3. End of the match
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102 4. ID of the match
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103 5. Length of the match
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104 6. Strand
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105 7. Matched sequence as it appears on the forward strand
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106
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107 For matches on the reverse strand it is reported the start and end position on the
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108 forward strand and the matched string on the forward strand (so the G4 'GGGAGGGT'
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109 present on the reverse strand is reported as ACCCTCCC).
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110
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111
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112 Note: Fasta sequences (chroms) are read in memory one at a time along with the
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113 matches for that chromosome.
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114 The order of the output is: chroms as they are found in the inut fasta, matches
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115 sorted within chroms by positions.
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116
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117 ARGUMENTS:
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118
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119 - regex Regex to be searched in the fasta input. Matches to the reverse complement will have - strand. The default regex is '([gG]{3,}\w{1,7}){3,}[gG]{3,}' which searches for G-quadruplexes.
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120 - matchcase Match case while searching for matches. Default is to ignore case (I.e. 'ACTG' will match 'actg').
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121 - noreverse Do not search the reverse complement of the input fasta. Use this flag to search protein sequences.
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122 - maxstr Maximum length of the match to report in the 7th column of the output. Default is to report up to 10000nt. Truncated matches are reported as <ACTG...ACTG>[<maxstr>,<tot length>]
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123 - seqnames List of fasta sequences in the input to search. E.g. use --seqnames chr1 chr2 chrM to search only these crhomosomes. Default is to search all the sequences in input.
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124
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125 EXAMPLE:
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126
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127 Test data::
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128 >mychr
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129 ACTGnACTGnACTGnTGAC
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130
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131 Example1 regex=ACTG::
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132
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133 mychr 0 4 mychr_0_4_for 4 + ACTG
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134 mychr 5 9 mychr_5_9_for 4 + ACTG
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135 mychr 10 14 mychr_10_14_for 4 + ACTG
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136
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137 Example2 regex=ACTG maxstr=3::
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138
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139 mychr 0 4 mychr_0_4_for 4 + ACT[3,4]
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140 mychr 5 9 mychr_5_9_for 4 + ACT[3,4]
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141 mychr 10 14 mychr_10_14_for 4 + ACT[3,4]
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142
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143 Example3 regex=A\w\wG::
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144
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145 mychr 0 5 mychr_0_5_for 5 + ACTGn
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146 mychr 5 10 mychr_5_10_for 5 + ACTGn
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147 mychr 10 15 mychr_10_15_for 5 + ACTGn
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148
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149 ]]></help>
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150 <citations>
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151 <citation type="bibtex">
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152 @misc{githubfastaRegexFinder,
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153 author = {Dario Beraldi},
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154 year = {2017},
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155 title = {fastaRegexFinder},
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156 publisher = {GitHub},
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157 journal = {GitHub repository},
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158 url = {https://github.com/dariober/bioinformatics-cafe/tree/master/fastaRegexFinder},
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159 }</citation>
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160 </citations>
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161 </tool>