Mercurial > repos > iuc > smgu_frameshift_deletions_checks
annotate frameshift_deletions_checks.xml @ 0:f079716f598c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
author | iuc |
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date | Wed, 31 May 2023 17:10:11 +0000 |
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children | 029d90b0c4f6 |
rev | line source |
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0
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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1 <tool id="smgu_frameshift_deletions_checks" name="Frameshift Deletions Checks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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2 <description>reports on frameshifting indels in consensus sequence</description> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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3 <macros> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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4 <import>macros.xml</import> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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5 </macros> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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6 <expand macro="xrefs"/> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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7 <requirements> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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8 <requirement type="package" version="@TOOL_VERSION@">smallgenomeutilities</requirement> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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9 </requirements> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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10 <!-- once we have version-from-git-tag in 0.4.0: <version_command>frameshift_deletion_checks --version</version_command> --> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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11 <command detect_errors="exit_code"> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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12 <![CDATA[ |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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13 #if $input.is_of_type("cram"): |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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14 echo 'is CRAM' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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15 ln -vs '$input' 'input.${input.ext}' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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16 ln -vs '$input.metadata.cram_index' 'input.${input.ext}.crai' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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17 #elif $input.is_of_type("bam"): |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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18 echo 'is BAM' && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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19 ln -s '$input' 'input.${input.ext}' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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20 ln -s '$input.metadata.bam_index' 'input.${input.ext}.bai' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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21 #else: |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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22 # raise TypeError('Unknown input alignment type ${input.ext}') |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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23 #end if |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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24 ln -vs '$consensus' 'consensus.${consensus.ext}' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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25 ln -vs '$reference' 'reference.${reference.ext}' >&2 && |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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26 |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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27 frameshift_deletions_checks |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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28 --input='input.${input.ext}' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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29 --consensus='consensus.${consensus.ext}' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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30 --reference='reference.${reference.ext}' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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31 --genes='$genes' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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32 --output='$report' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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33 #if $orf1ab != '': |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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34 --orf1ab='$orf1ab' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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35 #end if |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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36 '$english' |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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37 $zero_based |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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38 ]]> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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39 <!-- ##cores \${GALAXY_SLOTS:-4} --> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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40 </command> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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41 <inputs> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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42 <param argument="--consensus" type="data" format="fasta" label="Consensus" help="Fasta file containing the sample's consensus sequence (majority, with indels)" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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43 <param argument="--input" type="data" format="bam,cram" label="Input BAM" help="Input BAM file with sample's sequencing reads, aligned against the reference" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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44 <param argument="--reference" type="data" format="fasta" label="Reference" help="Fasta file containing the reference sequence (used during alignment) to compare against" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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45 <param argument="--genes" type="data" format="gff" label="Genes GFF" help="GFF file listing genes positions on the reference sequence" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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46 |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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47 <param argument="--english" type="boolean" truevalue="--english" falsevalue="--no-english" checked="true" optional="true" label="Write Summary Diagnosis?" help="If checked writes english summary diagnosis." /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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48 <param argument="--zero-based" type="boolean" truevalue="--zero-based" falsevalue="" checked="false" optional="true" label="Use 0-based Sequence Positions?" help="Use 0-based (python) instead of 1-based (standard) seq positions" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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49 <param argument="--orf1ab" type="text" value="cds-YP_009724389.1" optional="true" label="ORF1AB" help="CDS ID for the full Orf1ab CDS, comprising the ribosomal shift. In the GFF this CDS should consist of 2 entries with the same CDS ID due to the partial overlap caused by the ribosomal shift at translation time."/> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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50 </inputs> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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51 <outputs> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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52 <data name="report" format="tabular" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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53 </outputs> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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54 <tests> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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55 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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56 <param name="consensus" value="consensus.bcftools.fasta.gz" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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57 <param name="input" value="REF_aln_trim.cram" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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58 <param name="reference" value="NC_045512.2.fasta.gz" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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59 <param name="genes" value="Genes_NC_045512.2.GFF3" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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60 <output name="report" value="frameshift_deletions_check.tsv" /> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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61 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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62 </tests> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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63 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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64 <![CDATA[ |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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65 Produces a report about frameshifting indels in a consensus sequences. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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66 |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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67 Developed as part of the `V-pipe workflow for analysing NGS data of short viral genomes <https://github.com/cbg-ethz/V-pipe>`_. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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68 |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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69 Columns signification: |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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70 ---------------------- |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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71 |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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72 * *gene_region*: Gene in which the deletion is found according to ``--genes`` argument; |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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73 * *reads_all*: Total number of reads covering the indel; |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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74 * *reads_fwd*: Total nubmer of forward reads covering the indel; |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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75 * *reads_rev*: Total nubmer of reverse reads covering the indel; |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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76 * *deletions/insertions*: Number of reads supporting the deletion/insertion; |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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77 * *freq_del/freq_insert*: Fraction of reads supporting the deletion/insertion; |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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78 * *matches_ref*: number of reads that matche with the reference base; |
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79 * *pos_critical_inserts*: Start positions of insertions in the same gene_region that occur in > 40% of reads; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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80 * *pos_critical_dels*: Start positions of deletions in the same gene_region that occur in > 40% of reads; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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81 * *homopolymeric*: True if either around the start or end position of the deletion three bases are the same, which may have caused the polymerase to skip during reverse transcription of viral RNA to cDNA, e.g. AATAG; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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82 * *ref_base*: base in the reference genome; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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83 * *indel_position_english*: english sentence describing the indel; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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84 * *indel_diagnosis*: english sentence with the indel diagnosis; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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85 * *orf1ab*: CDS ID for the full Orf1ab CDS, comprising the ribosomal shift. In the GFF this CDS should consist of 2 entries with the same CDS ID due to the parital overlap caused by the ribosomal shift at translation time |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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86 ]]> |
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87 </help> |
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88 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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89 </tool> |