Mercurial > repos > iuc > irissv
annotate irissv.xml @ 2:b4b6b660293a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
author | iuc |
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date | Wed, 06 Jul 2022 07:07:21 +0000 |
parents | 1d4f065fa0ef |
children | 3242dbeea69c |
rev | line source |
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2
b4b6b660293a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents:
1
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changeset
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1 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> |
0
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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2 <description>Refine insertion sequences</description> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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3 <macros> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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5 </macros> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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6 |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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7 <expand macro="requirements"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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8 <expand macro="version_command"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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9 |
2
b4b6b660293a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents:
1
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10 <command detect_errors="aggressive"><![CDATA[ |
0
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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11 @REF_FASTA@ |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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12 |
2
b4b6b660293a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents:
1
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changeset
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13 ln -s '$in_bam' reads.bam && |
b4b6b660293a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents:
1
diff
changeset
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14 ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' && |
b4b6b660293a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents:
1
diff
changeset
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15 |
0
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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16 iris |
1
1d4f065fa0ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
iuc
parents:
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17 genome_in=reference |
0
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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18 vcf_in='${in_vcf}' |
2
b4b6b660293a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents:
1
diff
changeset
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19 reads_in='reads.bam' |
0
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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20 vcf_out='${out_vcf}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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21 threads=\${GALAXY_SLOTS:-4} |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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22 padding_before='${padding_before}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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23 padding_after='${padding_after}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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24 genome_buffer='${genome_buffer}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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25 min_ins_length='${min_ins_length}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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26 max_ins_dist='${max_ins_dist}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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27 max_out_length='${max_out_length}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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28 max_len_change='${max_len_change}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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29 '${aligner}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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30 '${rerunracon}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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31 '${also_deletions}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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32 '${keep_long_variants}' |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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33 ]]></command> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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34 <inputs> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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35 <!-- |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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36 Required arguments |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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37 --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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38 <expand macro="reference"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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39 <param name="in_vcf" type="data" format="vcf" label="The VCF file with variant calls/supporting reads"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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40 <param name="in_bam" type="data" format="bam" label="The BAM file containing the reads"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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41 <!--log_out param doesn't seem to produce output for some reason, commenting out.--> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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42 <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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43 <!-- |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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44 Optional arguments |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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45 --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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46 <param argument="padding_before" type="integer" value="1" min="1" label="The number of bases to output before the variant in REF/ALT fields" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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47 <param argument="padding_after" type="integer" value="0" min="0" label="The number of bases to output after the variant in REF/ALT fields" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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48 <param argument="genome_buffer" type="integer" value="100000" min="1" label="The genome region on each side of the SV to align assembled reads to" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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49 <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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50 <param argument="max_ins_dist" type="integer" value="100" min="0" label="The max distance a refined insertion call can be from its old position" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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51 <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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52 <param argument="max_len_change" type="float" value="0.25" min="0.0" label="The max proportion by which a variant's length can change" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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53 |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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54 <param name="aligner" type="select"> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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55 <option value="" selected="true">Use minimap2 for mapping</option> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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56 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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57 <option value="--hifi">Use minimap2 in hifi mode</option> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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58 </param> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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59 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" /> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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60 <!-- |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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61 Flags |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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62 --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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63 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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64 <param argument="--keep_long_variants" type="boolean" truevalue="--keep_long_variants" falsevalue="" checked="false" label="output original VCF line for very long variants instead of ignoring them"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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65 </inputs> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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66 <outputs> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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67 <!-- standard --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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68 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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69 <!--log_out param doesn't seem to produce output for some reason, commenting out.--> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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70 <!-- <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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71 <filter>output_log</filter> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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72 </data> --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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73 </outputs> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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74 <tests> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
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75 <!-- #1 default --> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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76 <test expect_num_outputs="1"> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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77 <conditional name="reference_source"> |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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78 <param name="reference_source_selector" value="history"/> |
1
1d4f065fa0ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
iuc
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0
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79 <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/> |
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80 </conditional> |
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81 <param name="in_vcf" value="sniffles.vcf"/> |
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82 <param name="in_bam" value="iris.bam"/> |
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83 <output name="out_vcf" file="test_out.vcf"/> |
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84 </test> |
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85 <test expect_num_outputs="1"> |
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86 <conditional name="reference_source"> |
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87 <param name="reference_source_selector" value="cached"/> |
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88 <param name="ref_file" value="iris"/> |
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89 </conditional> |
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90 <param name="in_vcf" value="sniffles.vcf"/> |
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91 <param name="in_bam" value="iris.bam"/> |
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92 <output name="out_vcf" file="test_out.vcf"/> |
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93 </test> |
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94 </tests> |
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95 <help><![CDATA[ |
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96 .. class:: infomark |
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97 |
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98 **What it does** |
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99 |
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100 @WID@ |
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101 |
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102 |
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103 **Input** |
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104 |
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105 - FASTA file containing the reference genome |
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106 |
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107 - VCF file with variant calls & supporting reads determined by Sniffles |
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108 |
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109 - BAM file containing the reads |
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110 |
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111 **Output** |
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112 |
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113 - VCF file with refined insertion sequences |
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114 |
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115 **References** |
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116 |
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117 @REFERENCES@ |
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118 ]]></help> |
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119 <expand macro="citations"/> |
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120 </tool> |