Mercurial > repos > iuc > cooc_mutbamscan
annotate cooc_mutbamscan.xml @ 2:1098fed28f65 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 1d5ff6cf59878101c2c5c94882d76763b47e169b
author | iuc |
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date | Fri, 25 Aug 2023 19:28:47 +0000 |
parents | df723877bcd8 |
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rev | line source |
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90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
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1 <tool id="cooc_mutbamscan" name="Cojac: mutbamscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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diff
changeset
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2 profile="@PROFILE@"> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff
changeset
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3 <description> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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4 scans an alignment file for mutation co-occurrences |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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diff
changeset
|
5 </description> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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6 <macros> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
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7 <import>macros.xml</import> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
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8 </macros> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
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9 <expand macro="biotools"/> |
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df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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diff
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10 <expand macro="requirements"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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11 <requirement type="package" version="0.1.0">viramp-hub</requirement> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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12 </expand> |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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13 <expand macro="version"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
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14 <command detect_errors="exit_code"><![CDATA[ |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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diff
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15 ## arrange BAM inputs and index files into a V-pipe-style folder structure |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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16 ## that cojac understands |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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17 sh arrange_samples.sh && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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18 |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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19 #if $spec_layout.mode == 'separate': |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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20 #set $voc_config = $spec_layout.voc_source |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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21 @VOCDIR_COMMAND@ |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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22 ## prepare amplicon information |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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23 #if $spec_layout.amplicon_definitions.choice == 'insert_scheme': |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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24 ln -s '$spec_layout.amplicon_definitions.insert_bed' bed_cojac.bed && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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25 #else if $spec_layout.amplicon_definitions.choice == 'primer_scheme': |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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26 scheme-convert '$spec_layout.amplicon_definitions.primer_bed' -t bed -b cojac -o bed_cojac.bed && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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27 #else: |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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28 scheme-convert '$spec_layout.amplicon_definitions.primer_bed' -t bed -b cojac -a '$spec_layout.amplicon_definitions.amplicon_info' -o bed_cojac.bed && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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29 #end if |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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30 #end if |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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31 |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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32 ## run cojac |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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33 cojac cooc-mutbamscan |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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34 ## use a sample list file to tell cojac to look for the inputs in the |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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35 ## V-pipe-style folder stucture we've created earlier. |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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36 -s samples_list.tsv |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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37 -p inputs |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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38 -b bed_cojac.bed |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
changeset
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39 #if $spec_layout.mode == 'separate': |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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40 -m voc/ |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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41 -A amplicons.yaml |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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42 --cooc $spec_layout.cooc |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff
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43 #else |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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44 -Q '$spec_layout.in_amp' |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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45 #end if |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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46 #if 'yaml' in $out_opts.output_formats: |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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47 -y cooc.yaml |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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48 #end if |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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49 #if 'json' in $out_opts.output_formats: |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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50 -j cooc.json |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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51 #end if |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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52 #if 'tabular' in $out_opts.output_formats: |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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53 -t cooc.tsv |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff
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54 #end if |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
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55 ]]></command> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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56 <configfiles> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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57 <configfile filename="arrange_samples.sh"><![CDATA[#for $dataset in $mapped_input: |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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58 #set $sample_id = $dataset.element_identifier.replace("'", '_').replace('/', '_') |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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59 mkdir -p 'inputs/$sample_id/1/alignments/' && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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60 ln -s '$dataset' 'inputs/$sample_id/1/alignments/REF_aln.bam' && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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61 ln -s '$dataset.metadata.bam_index' 'inputs/$sample_id/1/alignments/REF_aln.bam.bai' && |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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62 #end for |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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63 #set $num_samples = len($mapped_input) |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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64 echo "Gathered $num_samples sample and index files for cojac to discover from a samples list." |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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65 ]]></configfile> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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66 <configfile filename="samples_list.tsv"><![CDATA[#for $dataset in $mapped_input: |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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67 #set $line = '\t'.join([$dataset.element_identifier.replace("'", '_').replace('/', '_'), '1', str($dataset)]) |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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68 $line |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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69 #end for]]></configfile> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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70 </configfiles> |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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71 <inputs> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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72 <param name="mapped_input" type="data" format="bam" multiple="true" label="Aligned reads input to analyze"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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73 <conditional name="spec_layout"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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74 <param name="mode" type="select" label="How would you like to provide amplicon and lineage information?"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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75 <option value="separate">Separately</option> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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76 <option value="combined">Combined</option> |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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77 </param> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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78 <when value="separate"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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79 <expand macro="vocdir_input"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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80 <conditional name="amplicon_definitions"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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81 <param name="choice" type="select" label="Format of amplicon definitions"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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82 <option value="insert_scheme">Amplicon insert scheme (Cojac-native format)</option> |
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83 <option value="primer_scheme">Primer scheme (with autodetection of grouping into amplicons)</option> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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84 <option value="primer_scheme_plus">Primer scheme and explicit amplicon grouping information</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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85 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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86 <when value="insert_scheme"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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87 <param name="insert_bed" type="data" format="bed" label="Amplicon insert scheme" help="BED dataset providing the positions of the amplicon inserts (i.e. excluding the primer sequences) on the reference sequence."/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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88 </when> |
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89 <when value="primer_scheme"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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90 <param name="primer_bed" type="data" format="bed" label="Primer scheme" help="The tool will attempt to autodetect the relationship between primers and amplicons based on the primer names."/> |
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91 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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92 <when value="primer_scheme_plus"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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93 <param name="primer_bed" type="data" format="bed" label="Primer scheme" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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94 <param name="amplicon_info" type="data" format="tabular" label="Primers to amplicons assignments" help ="This input should have one line of tab-separated primer names (as they appear in the primer scheme) per amplicon."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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95 </when> |
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96 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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97 <param argument="--cooc" type="integer" min="1" value="2" label="Minimum number of mutations required to co-occur on an amplicon"/> |
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98 <param name="output_cojac_ampl" type="boolean" checked="true" label="Produce combined per-amplicon lineage definition output" help="The tool can generate a YAML-formatted report of expected co-occurrences of mutations per amplicon and lineage. This output combines amplicon scheme and lineage definitions and can be used for rerunning the tool with identical configuration in 'Combined' mode. It is also a recommended input to the cojac pubmut tool so leave this option checked if you are intending to use this downstream tool."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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99 </when> |
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100 <when value="combined"> |
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101 <param name="in_amp" type="data" format="yaml" label="Combined per-amplicon lineage definitions" |
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102 help="YAML-formatted report of expected co-occurrences of mutations per amplicon and lineage generated by a previous run of the tool."/> |
0
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103 </when> |
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104 </conditional> |
1
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105 <section name="out_opts" title="Output options" expanded="true"> |
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106 <param name="output_formats" type="select" display="checkboxes" multiple="true" label="Produce output in these formats" |
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107 help="Please note that only yaml- and json-formatted results can be processed with the downstream pubmut and tabmut tools."> |
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108 <option value="yaml">YAML</option> |
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109 <option value="json" selected="true">JSON</option> |
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110 <option value="tabular">tabular</option> |
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111 </param> |
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112 </section> |
0
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113 </inputs> |
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114 <outputs> |
1
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115 <data name="cooc_yaml" format="yaml" from_work_dir="cooc.yaml" label="${tool.name} on ${on_string}: Mutation co-occurrence (yaml)"> |
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116 <filter>'yaml' in out_opts['output_formats']</filter> |
0
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117 </data> |
1
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118 <data name="cooc_json" format="json" from_work_dir="cooc.json" label="${tool.name} on ${on_string}: Mutation co-occurrence (json)"> |
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119 <filter>'json' in out_opts['output_formats']</filter> |
0
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120 </data> |
1
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121 <data name="cooc_tsv" format="tabular" from_work_dir="cooc.tsv" label="${tool.name} on ${on_string}: Mutation co-occurrence (tabular)"> |
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122 <filter>'tabular' in out_opts['output_formats']</filter> |
0
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123 </data> |
1
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124 <data name="amplicons" format="yaml" from_work_dir="amplicons.yaml" label="${tool.name} on ${on_string}: Combined per-amplicon lineage definitions"> |
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125 <filter>spec_layout['mode'] == 'separate' and spec_layout['output_cojac_ampl']</filter> |
0
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126 </data> |
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127 </outputs> |
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128 <tests> |
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129 <!-- Test 1: build yaml for amplicons from bed and voc/ --> |
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130 <test expect_num_outputs="4"> |
1
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131 <param name="mapped_input" value="tbam11.bam"/> |
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132 <conditional name="spec_layout"> |
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133 <conditional name="voc_source"> |
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134 <param name="choice" value="custom"/> |
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135 <param name="collection"> |
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136 <collection type="list"> |
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137 <element name="BA.1" ftype="yaml" value="omicron_ba1_mutations.yaml" /> |
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138 </collection> |
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139 </param> |
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140 </conditional> |
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141 <conditional name="amplicon_definitions"> |
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142 <param name="insert_bed" value="nCoV-2019.insert.V3.bed" ftype="bed"/> |
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143 </conditional> |
0
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144 </conditional> |
1
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145 <section name="out_opts"> |
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146 <param name="output_formats" value="yaml,json,tabular"/> |
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147 </section> |
0
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148 <output name="cooc_yaml" ftype="yaml"> |
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149 <assert_contents> |
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150 <has_text text="76_om1"/> |
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151 <has_text text="81_om1"/> |
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152 </assert_contents> |
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153 </output> |
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154 <output name="cooc_json" ftype="json"> |
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155 <assert_contents> |
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156 <has_text text="76_om1"/> |
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157 <has_text text="81_om1"/> |
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158 </assert_contents> |
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159 </output> |
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160 <output name="cooc_tsv" ftype="tabular"> |
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161 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
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162 <has_text text="76_om1"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
|
163 <has_text text="81_om1"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff
changeset
|
164 </assert_contents> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
|
165 </output> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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diff
changeset
|
166 <output name="amplicons" ftype="yaml"> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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diff
changeset
|
167 <assert_contents> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
|
168 <has_text text="76_om1"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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changeset
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169 <has_text text="81_om1"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff
changeset
|
170 </assert_contents> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
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changeset
|
171 </output> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff
changeset
|
172 </test> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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173 <!-- Test 2: configure via cojac yaml --> |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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|
174 <test expect_num_outputs="2"> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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175 <param name="mapped_input" value="tbam11.bam"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
changeset
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176 <conditional name="spec_layout"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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177 <param name="mode" value="combined"/> |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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178 <param name="in_amp" value="amplicons111.yaml"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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179 </conditional> |
1
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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180 <section name="out_opts"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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181 <param name="output_formats" value="yaml,tabular"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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182 </section> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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183 <output name="cooc_yaml" ftype="yaml"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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184 <assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
changeset
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185 <has_text text="76_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
changeset
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186 <has_text text="81_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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187 </assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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188 </output> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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189 <output name="cooc_tsv" ftype="tabular"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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190 <assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
changeset
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191 <has_text text="76_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
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192 <has_text text="81_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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193 </assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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194 </output> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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|
195 </test> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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196 <!-- Test 3: use computed cojac format amplicon definitions from 2 files --> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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diff
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197 <test expect_num_outputs="2"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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198 <param name="mapped_input" value="tbam11.bam"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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199 <conditional name="spec_layout"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
changeset
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200 <conditional name="voc_source"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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201 <param name="choice" value="builtin"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
changeset
|
202 </conditional> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
0
diff
changeset
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203 <conditional name="amplicon_definitions"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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204 <param name="choice" value="primer_scheme_plus"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
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205 <param name="primer_bed" value="primers.bed" ftype="bed"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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206 <param name="amplicon_info" value="ampl_info.tsv"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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diff
changeset
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207 </conditional> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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208 <param name="output_cojac_ampl" value="false"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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209 </conditional> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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210 <section name="out_opts"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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211 <param name="output_formats" value="yaml,tabular"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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changeset
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212 </section> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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213 <output name="cooc_yaml" ftype="yaml"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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214 <assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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215 <has_text text="76_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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216 <has_text text="81_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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217 </assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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218 </output> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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219 <output name="cooc_tsv" ftype="tabular"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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220 <assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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221 <has_text text="76_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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222 <has_text text="81_om1"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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223 </assert_contents> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
parents:
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224 </output> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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225 </test> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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226 <!-- Test 4: test primer scheme as input --> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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227 <test expect_num_outputs="2"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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228 <param name="mapped_input" value="tbam11.bam"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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229 <conditional name="spec_layout"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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230 <conditional name="voc_source"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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231 <param name="choice" value="builtin"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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232 </conditional> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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233 <conditional name="amplicon_definitions"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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234 <param name="choice" value="primer_scheme"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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235 <param name="primer_bed" value="primers.bed" ftype="bed"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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236 </conditional> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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237 <param name="output_cojac_ampl" value="false"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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238 </conditional> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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239 <section name="out_opts"> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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240 <param name="output_formats" value="yaml,tabular"/> |
df723877bcd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
iuc
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241 </section> |
0
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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242 <output name="cooc_yaml" ftype="yaml"> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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243 <assert_contents> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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244 <has_text text="76_om1"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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245 <has_text text="81_om1"/> |
90d4dfb2d266
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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246 </assert_contents> |
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247 </output> |
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248 <output name="cooc_tsv" ftype="tabular"> |
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249 <assert_contents> |
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250 <has_text text="76_om1"/> |
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251 <has_text text="81_om1"/> |
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252 </assert_contents> |
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253 </output> |
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254 </test> |
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255 </tests> |
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256 <help><![CDATA[ |
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257 @HELP_HEADER@ |
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258 |
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259 Information about **cojac cooc-mutbamscan** |
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260 =========================================== |
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261 |
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262 The tool scans an alignment BAM/CRAM/SAM file for mutation co-occurrences. |
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263 It can report its findings in json, yaml and/or tabular format. |
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264 ]]></help> |
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265 <expand macro="citations"/> |
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266 </tool> |