Mercurial > repos > iuc > flash
annotate flash.xml @ 1:d043b54b3bfb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
author | iuc |
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date | Wed, 04 Oct 2017 16:03:42 -0400 |
parents | 13e98e2709b8 |
children | b48895989d78 |
rev | line source |
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13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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changeset
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1 <?xml version="1.0"?> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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2 <tool id="flash" name="FLASH" version="@VERSION@.1"> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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changeset
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3 <description>adjust length of short reads</description> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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4 <requirements> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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5 <requirement type="package" version="@VERSION@">flash</requirement> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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diff
changeset
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6 </requirements> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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7 <macros> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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8 <token name="@VERSION@">1.2.11</token> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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9 </macros> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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10 <version_command>flash --version | head -n 1</version_command> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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changeset
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11 <command detect_errors="aggressive"> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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12 <![CDATA[ |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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changeset
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13 flash --threads=\${GALAXY_SLOTS:-1} |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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14 -m $min_overlap |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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15 -M $max_overlap |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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16 -x $max_mismatch_density |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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17 $allow_outies |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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18 #if $layout.select_layout == 'individual': |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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changeset
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19 '$layout.forward' '$layout.reverse' |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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20 #else: |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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diff
changeset
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21 '$layout.reads.forward' '$layout.reads.reverse' |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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22 #end if |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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23 ]]> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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changeset
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24 </command> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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changeset
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25 <inputs> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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changeset
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26 <conditional name="layout"> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
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27 <param name="select_layout" type="select"> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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changeset
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28 <option value="individual">Individual datasets</option> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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changeset
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29 <option value="collection">Paired collection</option> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
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30 </param> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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changeset
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31 <when value="individual"> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
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32 <param format="fastq" name="forward" type="data" label="Forward reads" /> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
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33 <param format="fastq" name="reverse" type="data" label="Reverse reads" /> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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34 </when> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
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35 <when value="collection"> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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36 <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Read collection" /> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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37 </when> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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38 </conditional> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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changeset
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39 <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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40 <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
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41 <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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changeset
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42 <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." /> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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43 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" /> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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44 </inputs> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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45 <outputs> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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46 <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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47 <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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48 <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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49 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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50 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram"> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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51 <filter>generate_histogram</filter> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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52 </data> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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53 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" > |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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54 <filter>allow_outies</filter> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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55 </data> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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56 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" > |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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57 <filter>allow_outies</filter> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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58 </data> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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59 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" > |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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60 <filter>allow_outies and generate_histogram</filter> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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61 </data> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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62 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" > |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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63 <filter>allow_outies and generate_histogram</filter> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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64 </data> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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65 </outputs> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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66 <tests> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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67 <test> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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68 <param name="forward" value="flash_forward_in1.fastq" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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69 <param name="reverse" value="flash_reverse_in1.fastq" /> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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70 <param name="generate_histogram" value="false" /> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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71 <output name="merged_reads" file="flash_merged_out1.fastq" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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72 <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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73 <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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74 <output name="hist" file="flash_hist_out1.tabular" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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75 </test> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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76 <test> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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77 <param name="forward" value="flash_forward_in2.fastq" /> |
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78 <param name="reverse" value="flash_reverse_in2.fastq" /> |
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79 <param name="allow_outies" value="true" /> |
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80 <param name="generate_histogram" value="true" /> |
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81 <output name="merged_reads" file="flash_merged_out2.fastq" /> |
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82 <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" /> |
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83 <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" /> |
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84 <output name="hist" file="flash_hist_out2.tabular" /> |
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85 <output name="histogram" file="flash_hist_out2.txt" /> |
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86 <output name="hist_in" file="flash_hist_in_out2.tabular" /> |
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87 <output name="histogram_in" file="flash_hist_in_out2.txt" /> |
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88 <output name="hist_out" file="flash_hist_out_out2.tabular" /> |
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89 <output name="histogram_out" file="flash_hist_out_out2.txt" /> |
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90 </test> |
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91 </tests> |
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92 <help> |
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93 <![CDATA[ |
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94 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool |
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95 to merge paired-end reads that were generated from DNA fragments whose |
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96 lengths are shorter than twice the length of reads. Merged read pairs result |
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97 in unpaired longer reads, which are generally more desired in genome |
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98 assembly and genome analysis processes. |
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99 |
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100 Briefly, the FLASH algorithm considers all possible overlaps at or above a |
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101 minimum length between the reads in a pair and chooses the overlap that |
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102 results in the lowest mismatch density (proportion of mismatched bases in |
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103 the overlapped region). Ties between multiple overlaps are broken by |
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104 considering quality scores at mismatch sites. When building the merged |
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105 sequence, FLASH computes a consensus sequence in the overlapped region. |
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106 ]]> |
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107 </help> |
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108 <citations> |
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109 <citation type="doi">10.1093/bioinformatics/btr507</citation> |
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110 </citations> |
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111 </tool> |