Mercurial > repos > artbio > manta
annotate manta_macros.xml @ 7:555971edd46e draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
| author | artbio |
|---|---|
| date | Tue, 20 Feb 2024 08:31:27 +0000 |
| parents | cb5691381acb |
| children |
| rev | line source |
|---|---|
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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changeset
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1 <macros> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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2 |
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6
cb5691381acb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
artbio
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5
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3 <token name="@TOOL_VERSION@">1.6</token> |
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7
555971edd46e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff
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4 <token name="@VERSION_SUFFIX@">9</token> |
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555971edd46e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
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diff
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5 <token name="@PROFILE@">20.05</token> |
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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6 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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7 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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8 <token name="@set_reference_fasta_filename@"><![CDATA[ |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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9 #set $reference_fasta_filename = "localref.fa" |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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10 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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11 #if str( $reference_source.reference_source_selector ) == "history": |
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7
555971edd46e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
6
diff
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12 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && |
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555971edd46e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
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diff
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13 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 && |
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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14 #else: |
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7
555971edd46e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
6
diff
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15 #set $reference_fasta_filename = str( $reference_source.index.fields.path ) |
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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16 #end if |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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17 ]]></token> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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18 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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19 <token name="@set_configuration_file@"><![CDATA[ |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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20 #if str( $configuration.configuration_switch ) == "Custom_config_file": |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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21 #set $config_file = '$configuration.CustomConfigFile' |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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22 #else if str( $configuration.configuration_switch )== "Customized": |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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23 #set $config_file = '$configuration.Customized' |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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24 #else: |
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3
d648e40c6da9
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents:
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25 #set $config_file = 'configManta.py.ini' |
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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26 #end if |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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27 ]]></token> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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28 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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29 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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30 <xml name="requirements"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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31 <requirements> |
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7
555971edd46e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
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diff
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32 <requirement type="package" version="@TOOL_VERSION@">manta</requirement> |
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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33 <requirement type="package" version="1.7">samtools</requirement> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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34 </requirements> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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35 </xml> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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36 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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37 <xml name="stdio"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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38 <stdio> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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39 <exit_code range="1:" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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40 <exit_code range=":-1" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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41 <regex match="Error:" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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42 <regex match="Exception:" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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43 <regex match="\[bns_restore_core\] Parse error reading" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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44 </stdio> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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45 </xml> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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46 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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47 <macro name="reference_source_conditional"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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48 <conditional name="reference_source"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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49 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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50 <option value="cached">Use a built-in genome index</option> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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51 <option value="history">Use a genome from history and build index</option> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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52 </param> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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53 <when value="cached"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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54 <param name="index" type="select" label="Using reference genome" help="Select genome from the list"> |
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2
6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
1
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55 <options from_data_table="fasta_indexes"> |
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0
42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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56 <filter type="sort_by" column="2" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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57 <validator type="no_options" message="No indexes are available" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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58 </options> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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59 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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60 </param> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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61 </when> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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62 <when value="history"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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63 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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64 help="You can upload a FASTA sequence to the history and use it as reference" /> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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65 </when> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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66 </conditional> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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67 </macro> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
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68 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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69 <macro name="manta_configuration"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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70 <conditional name="configuration"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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71 <param name="configuration_switch" type="select" label="How do you want to configure manta?"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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72 <option value="Custom_config_file">Upload a different config file</option> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
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73 <option value="Customized">Customize the options</option> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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74 </param> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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75 <when value="Custom_config_file"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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76 <param format="ini" name="CustomConfigFile" type="data" label="config file"/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff
changeset
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77 </when> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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78 <when value="Customized"> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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79 <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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80 <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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81 <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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82 <param name="graphNodeMaxEdgeCount" type="integer" value="10" label="graphNodeMaxEdgeCount" help="If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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83 <param name="minCandidateSpanningCount" type="integer" value="3" label="minCandidateSpanningCount" help="Run discovery and candidate reporting for all SVs/indels with at least this many spanning support observations."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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84 <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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85 <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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86 <param name="minPassDiploidVariantScore" type="integer" value="20" label="minPassDiploidVariantScore" help="VCF 'QUAL' score below which a variant is marked as filtered in the diploid vcf."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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87 <param name="minPassDiploidGTScore" type="integer" value="15" label="minPassDiploidGTScore" help="Minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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88 <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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89 <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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90 <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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91 <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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92 <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value <= 0 to skip overlapping read pairs."/> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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93 </when> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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94 </conditional> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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95 </macro> |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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96 |
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42ba283a0fe2
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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97 </macros> |