Mercurial > repos > iuc > flash
annotate flash.xml @ 5:a27654fc4270 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
author | iuc |
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date | Wed, 03 Apr 2019 19:49:20 -0400 |
parents | c85bdba47254 |
children | 01a4ebf1f237 |
rev | line source |
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0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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1 <?xml version="1.0"?> |
5
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
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2 <tool id="flash" name="FLASH" version="@VERSION@.4"> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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3 <description>adjust length of short reads</description> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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4 <macros> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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5 <token name="@VERSION@">1.2.11</token> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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changeset
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6 </macros> |
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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7 <requirements> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
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8 <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
parents:
diff
changeset
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9 </requirements> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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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
parents:
diff
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
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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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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 $layout.select_layout == 'individual': |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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changeset
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19 '$layout.forward' '$layout.reverse' |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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changeset
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20 #set $input = $layout.forward |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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changeset
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21 #else: |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
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changeset
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22 '$layout.reads.forward' '$layout.reads.reverse' |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
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23 #set $input = $layout.reads.forward |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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changeset
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24 #end if |
5
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
changeset
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25 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz'): |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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26 -p 33 |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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changeset
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27 #else: |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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changeset
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28 -p 64 |
1
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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29 #end if |
5
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
changeset
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30 #if $input.ext.endswith('.gz'): |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
changeset
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31 -z |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
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32 #end if |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
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33 --output-suffix='' |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
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34 #if $save_log: |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
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35 > '$log' |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
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36 #end if |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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37 ]]> |
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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38 </command> |
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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39 <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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40 <conditional name="layout"> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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41 <param name="select_layout" type="select" label="Input data structure"> |
1
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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42 <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
diff
changeset
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43 <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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44 </param> |
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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45 <when value="individual"> |
5
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
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46 <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="forward" type="data" label="Forward reads" /> |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
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47 <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reverse" type="data" label="Reverse reads" /> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
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0
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48 </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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49 <when value="collection"> |
5
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
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50 <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> |
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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51 </when> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
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52 </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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53 <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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54 <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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55 <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:
diff
changeset
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56 <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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57 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" /> |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
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58 <param name="save_log" type="boolean" truevalue="" falsevalue="" checked="false" label="Save FLASH log file" /> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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59 </inputs> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
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60 <outputs> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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61 <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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62 <filter>layout['select_layout'] == 'collection'</filter> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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63 </data> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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64 <data format_source="reads['forward']" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
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65 <filter>layout['select_layout'] == 'collection'</filter> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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66 </data> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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67 <data format_source="reads['reverse']" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
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68 <filter>layout['select_layout'] == 'collection'</filter> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
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69 </data> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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70 <data format_source="forward" name="merged_paired_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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changeset
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71 <filter>layout['select_layout'] == 'individual'</filter> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
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72 </data> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
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73 <data format_source="forward" name="unmerged_paired_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
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74 <filter>layout['select_layout'] == 'individual'</filter> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
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75 </data> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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76 <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
77 <filter>layout['select_layout'] == 'individual'</filter> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
78 </data> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
79 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
80 <data format="txt" name="log" label="${tool.name} on ${on_string}: Raw Log"> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
81 <filter>raw_log == 'yes'</filter> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
82 </data> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
|
83 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram"> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
|
84 <filter>generate_histogram</filter> |
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
|
85 </data> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
86 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)"> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
87 <filter>allow_outies</filter> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
88 </data> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
89 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)"> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
90 <filter>allow_outies</filter> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
91 </data> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
92 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)"> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
|
93 <filter>allow_outies and generate_histogram</filter> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
94 </data> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
95 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${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
parents:
0
diff
changeset
|
96 <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:
diff
changeset
|
97 </data> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
98 </outputs> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
99 <tests> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
100 <test> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
101 <param name="select_layout" value="individual" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
102 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
103 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" /> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
|
104 <param name="generate_histogram" value="false" /> |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
105 <param name="save_log" value="true" /> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
106 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
107 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
108 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" /> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
109 <output name="hist" file="flash_hist_out1.tabular" /> |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
110 <output name="log"> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
111 <assert_contents> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
112 <has_line_matching expression=".*Percent combined: 3.60%" /> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
113 </assert_contents> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
114 </output> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
115 </test> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
116 <test> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
117 <param name="select_layout" value="individual" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
118 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
119 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" /> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
120 <param name="allow_outies" value="true" /> |
1
d043b54b3bfb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
iuc
parents:
0
diff
changeset
|
121 <param name="generate_histogram" value="true" /> |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
122 <param name="save_log" value="true" /> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
123 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
124 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
125 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" /> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
126 <output name="hist" file="flash_hist_out2.tabular" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
127 <output name="histogram" file="flash_hist_out2.txt" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
128 <output name="hist_in" file="flash_hist_in_out2.tabular" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
129 <output name="histogram_in" file="flash_hist_in_out2.txt" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
130 <output name="hist_out" file="flash_hist_out_out2.tabular" /> |
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
131 <output name="histogram_out" file="flash_hist_out_out2.txt" /> |
3
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
132 <output name="log"> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
133 <assert_contents> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
134 <has_line_matching expression=".*Percent combined: 3.80%" /> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
135 </assert_contents> |
dce033fd3c80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
iuc
parents:
2
diff
changeset
|
136 </output> |
0
13e98e2709b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents:
diff
changeset
|
137 </test> |
2
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
138 <test> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
139 <param name="select_layout" value="collection" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
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140 <param name="generate_histogram" value="false" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
141 <param name="reads"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
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142 <collection type="paired"> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
143 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
144 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
145 </collection> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
146 </param> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
147 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
148 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
149 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
150 <output name="hist" file="flash_hist_out3.tabular" /> |
b48895989d78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
1
diff
changeset
|
151 </test> |
5
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
changeset
|
152 <test> |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
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|
153 <param name="select_layout" value="individual" /> |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
changeset
|
154 <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" /> |
a27654fc4270
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
iuc
parents:
4
diff
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155 <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" /> |
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156 <param name="generate_histogram" value="false" /> |
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157 <param name="save_log" value="true" /> |
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158 <output name="merged_paired_reads" file="flash_merged_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> |
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159 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> |
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160 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> |
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161 <output name="log"> |
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162 <assert_contents> |
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163 <has_line_matching expression=".*Percent combined: 3.60%" /> |
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164 </assert_contents> |
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165 </output> |
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166 </test> |
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167 <test> |
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168 <param name="select_layout" value="collection" /> |
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169 <param name="generate_histogram" value="false" /> |
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170 <param name="reads"> |
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171 <collection type="paired"> |
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172 <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" /> |
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173 <element name="reverse" value="flash_reverse_in5.fastqsanger.gz" ftype="fastqsanger.gz" /> |
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174 </collection> |
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175 </param> |
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176 <output name="merged_reads" file="flash_merged_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> |
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177 <output name="unmerged_reads_f" file="flash_unmerged_f_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> |
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178 <output name="unmerged_reads_r" file="flash_unmerged_r_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> |
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179 <output name="hist" file="flash_hist_out5.tabular" /> |
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180 </test> |
0
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181 </tests> |
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182 <help> |
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183 <![CDATA[ |
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184 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool |
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185 to merge paired-end reads that were generated from DNA fragments whose |
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186 lengths are shorter than twice the length of reads. Merged read pairs result |
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187 in unpaired longer reads, which are generally more desired in genome |
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188 assembly and genome analysis processes. |
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189 |
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190 Briefly, the FLASH algorithm considers all possible overlaps at or above a |
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191 minimum length between the reads in a pair and chooses the overlap that |
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192 results in the lowest mismatch density (proportion of mismatched bases in |
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193 the overlapped region). Ties between multiple overlaps are broken by |
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194 considering quality scores at mismatch sites. When building the merged |
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195 sequence, FLASH computes a consensus sequence in the overlapped region. |
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196 ]]> |
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197 </help> |
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198 <citations> |
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199 <citation type="doi">10.1093/bioinformatics/btr507</citation> |
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200 </citations> |
2
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201 </tool> |