Mercurial > repos > iuc > colibread_discosnp_pp
annotate discosnp_pp.xml @ 5:e229f3c510aa draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author | iuc |
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date | Thu, 06 May 2021 12:41:13 +0000 |
parents | d3963fe808d1 |
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rev | line source |
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5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
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changeset
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1 <tool id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@"> |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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2 <description>is an efficient tool for detecting SNPs without a reference genome.</description> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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3 <macros> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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5 </macros> |
1
7fe259133cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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6 <expand macro="discosnp_requirements" /> |
5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
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7 <command detect_errors="exit_code"><![CDATA[ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
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8 #if str($input_type_options.input_type) == "single": |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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9 @discosnp_single_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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10 @single_reads@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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11 @discosnp_single_end_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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12 #else if str($input_type_options.input_type) == "paired": |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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13 @discosnp_paired_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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14 @paired_reads@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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15 @discosnp_paired_end_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
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16 #else: |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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17 @discosnp_single_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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18 @single_reads@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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19 @discosnp_single_end_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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20 @discosnp_paired_for@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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21 @paired_reads@ |
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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22 @discosnp_paired_end_for@ |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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23 #end if |
5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
changeset
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24 #if str($VCF_option.mapping) == 'reference': |
1
7fe259133cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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25 #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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26 ln -sf '${VCF_option.G}' '${reference_file}' && |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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27 #end if |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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28 run_discoSnp++.sh |
1
7fe259133cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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29 @discosnp_inputs@ |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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30 ${T} |
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d3963fe808d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
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31 -b ${b} |
5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
4
diff
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32 #if str($VCF_option.mapping) == 'reference': |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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33 -G '${reference_file}' |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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34 ${VCF_option.R} |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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35 #end if |
4
d3963fe808d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
parents:
1
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36 --max_threads \${GALAXY_SLOTS:-1} |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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37 ]]></command> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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38 <inputs> |
1
7fe259133cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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39 <expand macro="discosnp_inputs" /> |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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40 <param argument="-b" type="select" label="Branching strategy"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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41 <option value="0">variants for which any of the two paths is branching are discarded</option> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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42 <option value="1">forbid SNPs for wich the two paths are branching</option> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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43 <option value="2">No limitation on branching</option> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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44 </param> |
1
7fe259133cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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45 <expand macro="discosnp_options" /> |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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46 <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" /> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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47 <conditional name="VCF_option" > |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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48 <param name="mapping" type="select" label="VCF option"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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49 <option value="default">Do not use reference genome</option> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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50 <option value="reference">Mapping with a reference genome</option> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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51 </param> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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52 <when value="default"></when> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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53 <when value="reference"> |
5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
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54 <param argument="-G" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference genome file" /> |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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55 <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" /> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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56 </when> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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57 </conditional> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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58 </inputs> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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59 <outputs> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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60 <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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61 <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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62 </outputs> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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63 <tests> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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64 <test> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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65 <conditional name="input_type_options"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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66 <param name="input_type" value="single"/> |
5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
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67 <param name="list_reads" value="discosnp/reads1.gz,discosnp/reads2.gz" ftype="fasta.gz" /> |
0
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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68 </conditional> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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69 <param name="k" value="25"/> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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70 <output name="fasta" file="discosnp/multifasta.fa"/> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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71 <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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72 </test> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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73 <test> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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74 <conditional name="input_type_options"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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75 <param name="input_type" value="paired"/> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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76 <param name="list_paired_reads"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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77 <collection type="list:paired"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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78 <element name="Pair1"> |
91f0ee4e7f48
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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79 <collection type="paired"> |
5
e229f3c510aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
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80 <element name="forward" value="discosnp/reads1.gz" ftype="fasta.gz"/> |
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81 <element name="reverse" value="discosnp/reads2.gz" ftype="fasta.gz"/> |
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82 </collection> |
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83 </element> |
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84 </collection> |
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85 </param> |
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86 </conditional> |
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87 <conditional name="VCF_option"> |
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88 <param name="mapping" value="reference"/> |
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89 <param name="G" value="discosnp/reads1.gz" ftype="fasta.gz"/> |
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90 </conditional> |
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91 <output name="fasta" file="discosnp/multifasta_paired.fa"/> |
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92 <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/> |
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93 </test> |
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94 </tests> |
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95 <help><![CDATA[ |
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96 |
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97 **Description** |
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98 |
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99 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). |
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100 |
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101 Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed. |
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102 |
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103 The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism. |
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104 |
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105 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels. |
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106 |
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107 @discosnp_help@ |
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108 |
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109 ]]></help> |
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110 <expand macro="citations"> |
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111 <expand macro="discosnp_citation" /> |
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112 </expand> |
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113 </tool> |