Mercurial > repos > iuc > falco
annotate falco.xml @ 3:babbcf02d35c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
author | iuc |
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date | Tue, 10 Sep 2024 19:02:42 +0000 |
parents | eee1a2f6abd8 |
children | 959a14c1f2dd |
rev | line source |
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3
babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
iuc
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1 <tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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2 <description>An alternative, more performant implementation of FastQC for high throughput sequence quality control</description> |
3
babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
iuc
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3 <macros> |
babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
iuc
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4 <token name="@TOOL_VERSION@">1.2.3</token> |
babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
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5 <token name="@VERSION_SUFFIX@">0</token> |
babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
iuc
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6 </macros> |
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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 <xrefs> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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8 <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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9 </xrefs> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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10 <requirements> |
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babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
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11 <requirement type="package" version="@TOOL_VERSION@">falco</requirement> |
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e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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12 </requirements> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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13 <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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14 #import re |
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eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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15 #set input_name_sl = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) |
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e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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16 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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17 #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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18 #set format = 'bam' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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19 #elif 'sam' in $input_file.ext: |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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20 #set format = 'sam' |
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da336e3ead38
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 22e3bc5d61cdfec9938d42062d0f03766768c93f
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21 #elif 'gz' in $input_file.ext: |
da336e3ead38
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 22e3bc5d61cdfec9938d42062d0f03766768c93f
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22 #set format = 'fastq.gz' |
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e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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23 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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24 #set format = 'fastq' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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25 #end if |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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26 |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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27 ln -s '${input_file}' '${input_name_sl}' && |
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e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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28 falco |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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29 #if $contaminants: |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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30 --contaminants '${contaminants}' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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31 #end if |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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32 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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33 #if $adapters.dataset and str($adapters) > '' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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34 --adapters '${adapters}' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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35 #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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36 |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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37 #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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38 --limits '${limits}' |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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39 #end if |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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40 --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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41 --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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42 ## #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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43 ## --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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44 ## #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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45 $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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46 ## --kmers $kmers |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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47 -f '${format}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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48 '${input_name_sl}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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49 #if $subsample > 1: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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50 -subsample $subsample |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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51 #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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52 $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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53 $reverse_complement |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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54 $generate_summary |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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55 ]]></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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56 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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57 <param format="fastq,fastq.gz,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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58 <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
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59 <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
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60 <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."/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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61 <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!"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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62 <!-- 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
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63 <!-- 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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eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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64 <param argument="-subsample" type="integer" value="1" min="1" 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
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65 <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
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66 <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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babbcf02d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 900be4eec6ed42fd9addf229406458bb75e3d69b
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67 <param name="generate_summary" type="boolean" truevalue="" falsevalue="-skip-summary" checked="False" label="Generate summary output of QC test results"/> |
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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
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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 ${on_string}: Webpage"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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71 <data format="txt" name="text_file" from_work_dir="fastqc_data.txt" label="${tool.name} on ${on_string}: RawData"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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72 <data format="txt" name="summary_file" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: SummaryData"> |
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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73 <filter>generate_summary</filter> |
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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74 </data> |
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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 </outputs> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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76 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
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77 <test expect_num_outputs="2"> |
0
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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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changeset
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78 <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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changeset
|
79 <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
parents:
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changeset
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80 <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
parents:
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changeset
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81 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
parents:
1
diff
changeset
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82 <test expect_num_outputs="2"> |
0
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="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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84 <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
|
85 <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
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86 <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:
diff
changeset
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87 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
parents:
1
diff
changeset
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88 <test expect_num_outputs="2"> |
0
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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changeset
|
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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changeset
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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
parents:
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changeset
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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
parents:
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changeset
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93 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
parents:
1
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changeset
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94 <test expect_num_outputs="2"> |
0
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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95 <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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changeset
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96 <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
parents:
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changeset
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97 <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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98 <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
parents:
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changeset
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99 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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1
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100 <!-- ## The kmers param is ignored in Falco and always set to 7. If this ever gets reconsidered, this test could be uncommented. |
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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101 <test expect_num_outputs="2"> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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102 <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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changeset
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103 <param name="kmers" value="7"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
parents:
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104 <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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105 <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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106 <output name="text_file" file="fastqc_data_kmer.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 <assert_command> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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108 <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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109 </assert_command> |
e462044ece67
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110 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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111 ## The min_length param is not yet implemented in Falco. |
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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112 Once it is, this test may be uncommented. |
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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113 <test expect_num_outputs="2"> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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114 <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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115 <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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116 <output name="html_file" file="fastqc_report_min_length.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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117 <output name="text_file" file="fastqc_data_min_length.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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118 </test> --> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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119 <test expect_num_outputs="3"> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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120 <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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121 <param name="nogroup" value="--nogroup"/> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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122 <param name="generate_summary" value="true"/> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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123 <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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124 <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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125 <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
iuc
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126 <assert_command> |
e462044ece67
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127 <has_text text="--nogroup"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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128 </assert_command> |
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129 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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130 <test expect_num_outputs="3"> |
0
e462044ece67
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131 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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132 <param name="subsample" value="10"/> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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133 <param name="generate_summary" value="true"/> |
0
e462044ece67
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134 <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
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135 <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
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136 <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
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137 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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138 <test expect_num_outputs="3"> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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139 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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140 <param name="bisulfite" value="-bisulfite"/> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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141 <param name="generate_summary" value="true"/> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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142 <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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143 <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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144 <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
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145 </test> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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146 <test expect_num_outputs="3"> |
0
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
iuc
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147 <param name="input_file" value="1000trimmed.fastq"/> |
e462044ece67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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148 <param name="reverse_complement" value="-reverse-complement"/> |
2
eee1a2f6abd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit e1af25e42839c772b023f700210013658e42dc15
iuc
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149 <param name="generate_summary" value="true"/> |
0
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
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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
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153 </test> |
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154 </tests> |
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155 <help><![CDATA[ |
2
eee1a2f6abd8
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156 **What it does** |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c
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157 |
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158 Falco_ is a high-speed emulation of the popular FastQC software for quality control of sequencing data. |
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159 |
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160 💚️ With its superior performance Falco saves computational resources and gives you back results faster than FastQC. |
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161 |
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162 We recommend it for most use cases (but see below for exceptions). 💚️ |
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163 |
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164 The main functions of Falco are very similar to those of FastQC: |
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165 |
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166 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), |
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167 - Providing a quick overview to tell you in which areas there may be problems |
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168 - Summary graphs and tables to quickly assess your data |
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169 - Export of results to an HTML based permanent report |
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170 - Offline operation to allow automated generation of reports without running the interactive application |
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171 |
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172 .. class:: infomark |
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173 |
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174 The plain text report generated by Falco can be used as a "FastQC" report in MultiQC and its data is very similar though not 100% identical to that generated by FastQC on the same inputs. |
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175 |
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176 .. class:: Warning mark |
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177 |
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178 In the following situations, FastQC is still a better solution than this version of Falco: |
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179 |
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180 - your input is bz2-compressed fastq |
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181 |
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182 Falco doesn't currently support fastq.bz2 as input format meaning Galaxy has to perform a relatively slow format conversion before running the tool, which together makes the analysis slower than with FastQC. |
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183 |
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184 - you are interested in PolyA and PolyG statistics in the Adapter Content section of the quality report |
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185 |
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186 Falco doesn't currently calculate statistics for these "Adapters" by default. |
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187 |
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188 - your input consists of *mapped* reads in SAM/BAM format |
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189 |
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190 Due to a bug in the current version of Falco, reads mapped to the reverse strand of the reference genome are not handled correctly and reported metrics are wrong! |
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191 |
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192 ----- |
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193 |
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194 **Inputs and outputs** |
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195 |
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196 The Falco_ development repo includes very good documentation. |
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197 A summary of it follows below for those in a tearing hurry. |
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198 |
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199 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check. |
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200 It will also take an optional file containing a list of contaminants information, in the form of |
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201 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom |
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202 limits.txt file that allows setting the warning thresholds for the different modules and also specifies |
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203 which modules to include in the output. |
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204 |
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205 The tool produces a basic text and a HTML output file that contain all of the results, including the following: |
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206 |
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207 - Basic Statistics |
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208 - Per base sequence quality |
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209 - Per sequence quality scores |
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210 - Per base sequence content |
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211 - Per base GC content |
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212 - Per sequence GC content |
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213 - Per base N content |
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214 - Sequence Length Distribution |
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215 - Sequence Duplication Levels |
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216 - Overrepresented sequences |
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217 - Adapter Content |
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218 |
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219 All except Basic Statistics and Overrepresented sequences are plots. |
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220 .. _Falco: https://github.com/smithlabcode/falco/ |
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221 ]]></help> |
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222 <citations> |
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223 <citation type="doi">10.12688/f1000research.21142.2</citation> |
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224 </citations> |
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225 </tool> |