Mercurial > repos > iuc > falco
annotate falco.xml @ 0:e462044ece67 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
author | iuc |
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date | Tue, 04 Jun 2024 14:14:49 +0000 |
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children | da336e3ead38 |
rev | line source |
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0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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1 <tool id="falco" name="Falco" version="1.2.2+galaxy0" profile="21.05"> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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2 <description>A high throughput sequence QC analysis tool</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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3 <xrefs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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4 <xref type="bio.tools">falco</xref> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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5 </xrefs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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6 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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7 <requirement type="package" version="1.2.2">falco</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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8 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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9 <command detect_errors="aggressive"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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10 #import re |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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11 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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12 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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13 #if $input_file.ext.endswith('.gz'): |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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14 #set input_file_sl = $input_name + '.gz' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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15 #elif $input_file.ext.endswith('.bz2'): |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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16 #set input_file_sl = $input_name + '.bz2' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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17 #else |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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18 #set input_file_sl = $input_name |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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19 #end if |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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20 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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21 #if 'bam' in $input_file.ext: |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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22 #set format = 'bam' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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23 #elif 'sam' in $input_file.ext: |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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24 #set format = 'sam' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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25 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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26 #set format = 'fastq' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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27 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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28 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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29 ln -s '${input_file}' '${input_file_sl}' && |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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30 falco |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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31 #if $contaminants: |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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32 --contaminants '${contaminants}' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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33 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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34 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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35 #if $adapters.dataset and str($adapters) > '' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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36 --adapters '${adapters}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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37 #end if |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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38 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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39 #if $limits.dataset and str($limits) > '' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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40 --limits '${limits}' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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41 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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42 --threads \${GALAXY_SLOTS:-2} |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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43 --quiet |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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44 --extract |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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45 ## #if $min_length: |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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46 ## --min_length $min_length |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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47 ## #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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48 $nogroup |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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49 ## --kmers $kmers |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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50 -f '${format}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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51 '${input_file_sl}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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52 -subsample $subsample |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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53 $bisulfite |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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54 $reverse_complement |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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55 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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56 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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57 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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58 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data" label="Raw read data from your current history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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59 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list" help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer	CAAGCAGAAGACGGCATACGA"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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60 <param argument="--adapters" type="data" format="tabular" optional="true" label="Adapter list" help="List of adapters adapter sequences which will be explicity searched against the library. It should be a tab-delimited file with 2 columns: name and sequence."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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61 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file" help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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62 <param argument="--nogroup" type="boolean" truevalue="--nogroup" falsevalue="" checked="False" label="Disable grouping of bases for reads >50bp" help=" Using this option, your plots may end up a ridiculous size. You have been warned!"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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63 <!-- Not implemented in falco yet <param argument="-min_length" type="integer" value="" optional="true" label="Lower limit on the length of the sequence to be shown in the report" help=" [NOT YET IMPLEMENTED IN FALCO]. Sets an artificial lower limit on the length of the sequence to be shown in the report. As long as you set this to a value greater or equal to your longest read length then this will be the sequence length used to create your read groups. This can be useful for making directly comaparable statistics from datasets with somewhat variable read length."/> --> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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64 <!-- Ignored by falco and always set to 7 <param argument="-kmers" type="integer" value="7" min="2" max="10" label="Length of Kmer to look for" help="IGNORED BY FALCO AND ALWAYS SET TO 7. Specifies the length of Kmer to look for in the Kmer content module. Specified Kmer length must be between 2 and 10. Default length is 7 if not specified." /> --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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65 <param argument="-subsample" type="integer" value="1" min="1" optional="true" label="Subsampling Factor" help="This makes falco faster (but possibly less accurate) by only processing reads that are multiple of this value (using 0-based indexing to number reads)"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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66 <param argument="-bisulfite" type="boolean" truevalue="-bisulfite" falsevalue="" checked="False" label="Bisulfite Sequencing" help="This parameter indicates whether the reads are from whole genome bisulfite sequencing. When enabled, Falco will account for the expected increase in Ts and decrease in Cs in the base content."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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67 <param argument="reverse_complement" type="boolean" truevalue="-reverse-complement" falsevalue="" checked="False" label="Reverse Complement" help="This parameter specifies whether the input sequences are reverse-complemented. When enabled, all modules in Falco will be tested by swapping A/T and C/G."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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68 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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69 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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70 <data format="html" name="html_file" from_work_dir="fastqc_report.html" label="${tool.name} on ${on_string}: Webpage"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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71 <data format="txt" name="text_file" from_work_dir="fastqc_data.txt" label="${tool.name} on ${on_string}: RawData"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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72 <data format="txt" name="summary_file" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: SummaryData"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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73 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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74 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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75 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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76 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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77 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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78 <output name="text_file" file="fastqc_data.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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79 <output name="summary_file" file="summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
diff
changeset
|
80 </test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
diff
changeset
|
81 <test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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changeset
|
82 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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|
83 <param name="contaminants" value="contaminant_list.txt" ftype="tabular"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
diff
changeset
|
84 <output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
diff
changeset
|
85 <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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changeset
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86 <output name="summary_file" file="fastqc_data_contaminant_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
diff
changeset
|
87 </test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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changeset
|
88 <test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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89 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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90 <param name="adapters" value="adapter_list.txt" ftype="tabular"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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91 <output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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92 <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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93 <output name="summary_file" file="fastqc_data_adapters_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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changeset
|
94 </test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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changeset
|
95 <test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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96 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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97 <param name="limits" value="limits.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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98 <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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99 <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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100 <output name="summary_file" file="fastqc_data_customlimits_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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changeset
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101 </test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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102 <!-- ## This feature has not yet been implemented in Falco, but if it is, it may go uncommented in the future. |
e462044ece67
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iuc
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103 <test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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104 <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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105 <param name="kmers" value="7"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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106 <param name="limits" value="limits.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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107 <output name="html_file" file="fastqc_report_kmer.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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108 <output name="text_file" file="fastqc_data_kmer.txt" ftype="txt"/> |
e462044ece67
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iuc
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109 <output name="summary_file" file="fastqc_data_kmer_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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110 <assert_command> |
e462044ece67
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iuc
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111 <has_text text="kmers 7"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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112 </assert_command> |
e462044ece67
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iuc
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113 </test> |
e462044ece67
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114 |
e462044ece67
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115 <test> ##This feature is ignored in Falco and always set to 7. If this will be considered, may go uncommented in the future" |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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116 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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117 <param name="min_length" value="108"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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118 <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/> |
e462044ece67
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iuc
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119 <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/> |
e462044ece67
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120 <output name="summary_file" file="fastqc_data_min_length_summary.txt" ftype="txt"/> |
e462044ece67
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iuc
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121 </test> --> |
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122 |
e462044ece67
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iuc
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123 <test> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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124 <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/> |
e462044ece67
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iuc
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125 <param name="nogroup" value="--nogroup"/> |
e462044ece67
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iuc
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126 <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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127 <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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128 <output name="summary_file" file="fastqc_data_nogroup_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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129 <assert_command> |
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130 <has_text text="--nogroup"/> |
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131 </assert_command> |
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132 </test> |
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iuc
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133 <test> |
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134 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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135 <param name="subsample" value="10"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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136 <output name="html_file" file="fastqc_report_subsample.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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137 <output name="text_file" file="fastqc_report_subsample.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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138 <output name="summary_file" file="fastqc_report_subsample_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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139 </test> |
e462044ece67
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iuc
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140 <test> |
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141 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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142 <param name="bisulfite" value="-bisulfite"/> |
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iuc
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143 <output name="html_file" file="fastqc_report_bisulfite.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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144 <output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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145 <output name="summary_file" file="fastqc_report_bisulfite_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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|
146 </test> |
e462044ece67
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iuc
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147 <test> |
e462044ece67
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148 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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149 <param name="reverse_complement" value="-reverse-complement"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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150 <output name="html_file" file="fastqc_report_reverse_complement.html" ftype="html" lines_diff="2"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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151 <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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152 <output name="summary_file" file="fastqc_report_reverse_complement_summary.txt" ftype="txt"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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153 </test> |
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iuc
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154 </tests> |
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155 <help><![CDATA[ |
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156 .. class:: infomark |
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|
157 |
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iuc
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158 **Purpose** |
e462044ece67
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159 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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|
160 Falco is an emulation of the popular FastQC software to check large sequencing reads for common problems. |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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161 |
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162 The main functions of Falco are: |
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163 |
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164 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), |
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165 - Providing a quick overview to tell you in which areas there may be problems |
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166 - Summary graphs and tables to quickly assess your data |
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167 - Export of results to an HTML based permanent report |
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168 - Offline operation to allow automated generation of reports without running the interactive application |
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169 |
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170 ----- |
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171 |
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172 .. class:: infomark |
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173 |
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174 **Inputs and outputs** |
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175 |
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176 Falco_ is the best place to look for documentation - it's very good. |
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177 A summary follows below for those in a tearing hurry. |
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178 |
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179 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check. |
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180 It will also take an optional file containing a list of contaminants information, in the form of |
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181 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom |
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182 limits.txt file that allows setting the warning thresholds for the different modules and also specifies |
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183 which modules to include in the output. |
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184 |
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185 The tool produces a basic text and a HTML output file that contain all of the results, including the following: |
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186 |
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187 - Basic Statistics |
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188 - Per base sequence quality |
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189 - Per sequence quality scores |
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190 - Per base sequence content |
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191 - Per base GC content |
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192 - Per sequence GC content |
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193 - Per base N content |
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194 - Sequence Length Distribution |
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195 - Sequence Duplication Levels |
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196 - Overrepresented sequences |
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197 - Adapter Content |
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198 |
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199 All except Basic Statistics and Overrepresented sequences are plots. |
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200 .. _Falco: https://github.com/smithlabcode/falco/ |
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201 .. _Picard-tools: https://broadinstitute.github.io/picard/ |
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202 ]]></help> |
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203 <citations> |
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204 <citation type="bibtex"> |
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205 @article{deSenaBrandine2021, |
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206 author = {de Sena Brandine, Gabriel and Smith, Andrew D.}, |
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207 title = {Falco: high-speed FastQC emulation for quality control of sequencing data}, |
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208 journal = {F1000Research}, |
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209 year = {2021}, |
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210 volume = {8}, |
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211 pages = {1874}, |
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212 url = {https://doi.org/10.12688/f1000research.21142.2}, |
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213 doi = {10.12688/f1000research.21142.2}, |
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214 note = {Version 2; peer review: 2 approved}, |
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215 } |
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216 |
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217 </citation> |
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218 </citations> |
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219 </tool> |