Mercurial > repos > iuc > smgu_frameshift_deletions_checks
annotate frameshift_deletions_checks.xml @ 1:029d90b0c4f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
author | iuc |
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date | Fri, 14 Jul 2023 22:07:22 +0000 |
parents | f079716f598c |
children | e8971ca74398 |
rev | line source |
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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
iuc
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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
iuc
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3 <macros> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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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
iuc
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diff
changeset
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5 </macros> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
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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
iuc
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changeset
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7 <requirements> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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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
iuc
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9 </requirements> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
diff
changeset
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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
parents:
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changeset
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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
parents:
diff
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12 <![CDATA[ |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
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13 #if $input.is_of_type("cram"): |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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14 ln -s '$input' input.cram && |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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15 ln -s '$input.metadata.cram_index' input.cram.crai && |
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f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
diff
changeset
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16 #elif $input.is_of_type("bam"): |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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17 ln -s '$input' input.bam && |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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18 ln -s '$input.metadata.bam_index' input.bam.bai && |
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f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
diff
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19 #else: |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
diff
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20 # raise TypeError('Unknown input alignment type ${input.ext}') |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
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21 #end if |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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22 ln -s '$consensus' consensus.fasta && |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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23 #if str($ref_data.choice) == 'custom': |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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24 ln -s '$reference' reference.fa && |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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25 #else: |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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26 ln -s '$__tool_directory__/ref_NC_045512.2.fasta' reference.fa && |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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27 #end if |
0
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
diff
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28 |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
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29 frameshift_deletions_checks |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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30 --input=input.${input.ext} |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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31 --consensus=consensus.fasta |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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32 --reference=reference.fa |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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33 #if str($ref_data.choice) == 'standard': |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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34 --genes='$__tool_directory__'/annotations_NC_045512.2.gff3 |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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35 --orf1ab='cds-YP_009724389.1' |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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36 #else: |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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37 --genes='$ref_data.genes' |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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38 --orf1ab='$ref_data.orf1ab' |
0
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
diff
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39 #end if |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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40 $out_options.english |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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41 $out_options.zero_based |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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42 --output=report.tsv && |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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43 python '$__tool_directory__/frameshift_deletions_report_fixer.py' report.tsv '$report' |
0
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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44 ]]> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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45 <!-- ##cores \${GALAXY_SLOTS:-4} --> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
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46 </command> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
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47 <inputs> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
iuc
parents:
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48 <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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49 <param argument="--input" type="data" format="bam,cram" label="Input BAM" help="Input BAM file with sample's sequencing reads, aligned against the reference" /> |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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50 <conditional name="ref_data"> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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51 <param name="choice" type="select" label="Reference data selection" help="Select built-in genome files to base reported positions and annotations on the SARS-CoV-2 reference sequence NC_045512.2. If you have mapped to a different reference, select custom genome files and provide the reference sequence and genomic feature annotations for it in fasta and gff format, repsectively."> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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52 <option value="standard">Use built-in genome files</option> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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53 <option value="custom">Provide custom genome files</option> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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54 </param> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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55 <when value="standard" /> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
parents:
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56 <when value="custom"> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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57 <param argument="--reference" type="data" format="fasta" label="Reference" help="Fasta input containing the reference sequence (used during alignment) to compare against" /> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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58 <param argument="--genes" type="data" format="gff" label="Genes GFF" help="GFF input listing genes positions on the reference sequence" /> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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59 <param argument="--orf1ab" type="text" value="cds-YP_009724389.1" optional="false" label="Coding sequence containing ribosomal slippage site" help="ID of the full CDS comprising the ribosomal slippage site as it appears in the GFF input. 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. Hint: To use the tool with genomes that do not have a ribosomal slippage site, enter an ID that is not present in the GFF."> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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60 <validator type="expression">value.strip()</validator> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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61 </param> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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62 </when> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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63 </conditional> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
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64 <section name="out_options" title="Output format options" expanded="true"> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
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65 <param argument="--english" type="boolean" truevalue="--english" falsevalue="--no-english" checked="true" label="Write Summary Diagnosis?" help="If checked writes english summary diagnosis." /> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
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66 <param argument="--zero-based" type="boolean" truevalue="--zero-based" falsevalue="" checked="false" optional="true" label="Use 0-based Sequence Positions?" help="Use 0-based instead of 1-based genome positions" /> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
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67 </section> |
0
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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68 </inputs> |
f079716f598c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
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69 <outputs> |
1
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
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70 <data name="report" format="tabular"> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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71 <actions> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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72 <conditional name="out_options.english"> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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73 <!-- The "english" flag removes certain numerical columns and collapses them into new text columns --> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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74 <when value="--english"> |
029d90b0c4f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
iuc
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75 <action name="column_names" type="metadata" default="ref_id,start_position,length,VARIANT,gene_region,reads_all,reads_fwd,reads_rev,deletions,freq_del,freq_del_fwd,freq_del_rev,deletions_fwd,deletions_rev,insertions,freq_insert,freq_insert_fwd,freq_insert_rev,insertions_fwd,insertions_rev,stops,freq_stop,freq_stop_fwd,freq_stop_rev,stops_fwd,stops_rev,matches_ref,pos_critical_inserts,pos_critical_dels,homopolymeric,ref_base,cons_id,variant_position_english,variant_diagnosis" /> |
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76 </when> |
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77 <when value="--no-english"> |
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78 <action name="column_names" type="metadata" default="ref_id,start_position,length,VARIANT,gene_region,aa_position,stop_mismatches,stoploss_nt,reads_all,reads_fwd,reads_rev,deletions,freq_del,freq_del_fwd,freq_del_rev,deletions_fwd,deletions_rev,insertions,freq_insert,freq_insert_fwd,freq_insert_rev,insertions_fwd,insertions_rev,stops,freq_stop,freq_stop_fwd,freq_stop_rev,stops_fwd,stops_rev,matches_ref,pos_critical_inserts,pos_critical_dels,homopolymeric,ref_base,cons_id" /> |
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79 </when> |
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80 </conditional> |
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81 </actions> |
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82 </data> |
0
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83 </outputs> |
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84 <tests> |
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85 <test> |
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86 <param name="consensus" value="consensus.bcftools.fasta.gz" /> |
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87 <param name="input" value="REF_aln_trim.cram" /> |
1
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88 <conditional name="ref_data"> |
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89 <param name="choice" value="standard" /> |
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90 </conditional> |
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91 <output name="report" value="frameshift_deletions_check.tsv" /> |
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92 </test> |
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93 <test> |
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94 <param name="consensus" value="consensus.bcftools.fasta.gz" /> |
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95 <param name="input" value="REF_aln_trim.cram" /> |
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96 <conditional name="ref_data"> |
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97 <param name="choice" value="standard" /> |
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98 </conditional> |
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99 <section name="out_options"> |
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100 <param name="english" value="false" /> |
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101 </section> |
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102 <output name="report" value="frameshift_deletions_check_no_english.tsv" /> |
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103 </test> |
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104 <test> |
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105 <param name="consensus" value="consensus.bcftools.fasta.gz" /> |
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106 <param name="input" value="REF_aln_trim.cram" /> |
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107 <conditional name="ref_data"> |
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108 <param name="choice" value="custom" /> |
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109 <param name="reference" value="NC_045512.2.fasta" /> |
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110 <param name="genes" value="Genes_NC_045512.2.GFF3" /> |
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111 </conditional> |
0
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112 <output name="report" value="frameshift_deletions_check.tsv" /> |
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113 </test> |
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114 </tests> |
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115 <help> |
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116 <![CDATA[ |
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117 Produces a report about frameshifting indels in a consensus sequences. |
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118 |
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119 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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120 |
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121 Columns signification: |
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122 ---------------------- |
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123 |
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124 * *gene_region*: Gene in which the deletion is found according to ``--genes`` argument; |
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125 * *reads_all*: Total number of reads covering the indel; |
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126 * *reads_fwd*: Total number of forward reads covering the indel; |
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127 * *reads_rev*: Total number of reverse reads covering the indel; |
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128 * *deletions/insertions*: Number of reads supporting the deletion/insertion; |
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129 * *freq_del/freq_insert*: Fraction of reads supporting the deletion/insertion; |
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130 * *matches_ref*: number of reads that matche with the reference base; |
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131 * *pos_critical_inserts*: Start positions of insertions in the same gene_region that occur in > 40% of reads; |
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132 * *pos_critical_dels*: Start positions of deletions in the same gene_region that occur in > 40% of reads; |
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133 * *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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134 * *ref_base*: base in the reference genome; |
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135 * *indel_position_english*: english sentence describing the indel; |
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136 * *indel_diagnosis*: english sentence with the indel diagnosis; |
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137 * *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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138 ]]> |
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139 </help> |
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140 <expand macro="citations"/> |
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141 </tool> |