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annotate irma.xml @ 0:3d86c05cd838 draft

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planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
author iuc
date Sat, 09 Nov 2024 13:53:38 +0000
parents
children 736090e99c59
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0
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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1 <tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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2 <description>Construct robust assemblies of highly variable RNA viruses</description>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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3 <macros>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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4 <token name="@TOOL_VERSION@">1.2.0</token>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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6 </macros>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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7 <xrefs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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8 <xref type="bio.tools">irma-virus</xref>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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9 </xrefs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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10 <requirements>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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11 <requirement type="package" version="@TOOL_VERSION@">irma</requirement>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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12 <requirement type="package" version="3.12">python</requirement>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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13 </requirements>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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14 <command detect_errors="exit_code"><![CDATA[
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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15 ## handle gz inputs
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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16 #if $input_type == 'single'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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17 #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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18 ln -sf '${input_type_conditional.fastq_input1}' file1.fastq.gz &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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19 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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20 #elif $input_type == 'paired_collection'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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21 #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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22 ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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23 ln -sf '${input_type_conditional.fastq_input.reverse}' file2.fastq.gz &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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24 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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25 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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26
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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27 ## irma command
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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28 IRMA '${module}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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29 #if $input_type_conditional.input_type == 'single'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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30 #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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31 file1.fastq.gz
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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32 #else
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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33 '${input_type_conditional.fastq_input1}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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34 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
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35 #elif $input_type_conditional.input_type == 'paired_collection'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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36 #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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37 file1.fastq.gz
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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38 file2.fastq.gz
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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39 #else
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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40 '${input_type_conditional.fastq_input.forward}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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41 '${input_type_conditional.fastq_input.reverse}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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42 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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43 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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44 resultDir &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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45 ## IRMA does not write empty output files
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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46 ## so the following script makes sure all expected outputs exist unconditionally
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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47 python3 '$__tool_directory__/createMissingFiles.py' &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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48 cat irma_config.sh
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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49 ]]></command>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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50 <configfiles>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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51 <configfile filename='irma_config.sh'><![CDATA[
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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52 SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1}
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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53 DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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54 TMP=\$TMPDIR
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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55 #if $advanced_config.customize == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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56 #if $advanced_config.reference == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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57 SKIP_E=$advanced_config.reference.SKIP_E
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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58 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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59 #if $advanced_config.read_gathering == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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60 MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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61 USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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62 QUAL_THRESHOLD=$advanced_config.read_gathering.QUAL_THRESHOLD
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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63 MIN_LEN=$advanced_config.read_gathering.MIN_LEN
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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64 INCL_CHIM=$advanced_config.read_gathering.INCL_CHIM
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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65 ADAPTER=$advanced_config.read_gathering.ADAPTER
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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66 ENFORCE_CLIPPED_LENGTH=$advanced_config.read_gathering.ENFORCE_CLIPPED_LENGTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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67 MERGE_SECONDARY=$advanced_config.read_gathering.MERGE_SECONDARY
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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68 RESIDUAL_ASSEMBLY_FACTOR=$advanced_config.read_gathering.RESIDUAL_ASSEMBLY_FACTOR
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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69 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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70 #if $advanced_config.match_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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71 MIN_RP=$advanced_config.match_step.MIN_RP
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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72 MIN_RC=$advanced_config.match_step.MIN_RC
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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73 MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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74 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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75 #if $advanced_config.sort_step == 'yes':
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76 SORT_PROG=$advanced_config.sort_step.SORT_PROG
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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77 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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78 #if $advanced_config.align_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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79 ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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80 DEL_TYPE=$advanced_config.align_step.DEL_TYPE
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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81 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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82 #if $advanced_config.assembly == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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83 MAX_ITER_ASSEM=$advanced_config.assembly.MAX_ITER_ASSEM
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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84 NO_MERGE=$advanced_config.assembly.NO_MERGE
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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85 INS_T=$advanced_config.assembly.INS_T
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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86 DEL_T=$advanced_config.assembly.DEL_T
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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87 INS_T_DEPTH=$advanced_config.assembly.INS_T_DEPTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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88 DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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89 SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS
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90 MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG
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91 SSW_M=$advanced_config.assembly.SSW_M
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92 SSW_X=$advanced_config.assembly.SSW_X
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93 SSW_O=$advanced_config.assembly.SSW_O
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94 SSW_E=$advanced_config.assembly.SSW_E
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95 ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED
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96 #end if
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97 #if $advanced_config.variant_calling == 'yes':
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98 AUTO_F=$advanced_config.variant_calling.AUTO_F
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99 MIN_FI=$advanced_config.variant_calling.MIN_FI
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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100 MIN_FD=$advanced_config.variant_calling.MIN_FD
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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101 MIN_F=$advanced_config.variant_calling.MIN_F
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102 MIN_C=$advanced_config.variant_calling.MIN_C
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103 MIN_AQ=$advanced_config.variant_calling.MIN_AQ
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104 MIN_TCC=$advanced_config.variant_calling.MIN_TCC
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105 MIN_CONF=$advanced_config.variant_calling.MIN_CONF
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106 SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
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107 #end if
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108 #end if]]></configfile>
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109 </configfiles>
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110 <inputs>
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111 <conditional name="input_type_conditional">
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112 <param name="input_type" type="select" label="Input Type">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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113 <option value="single" selected="true">Single Dataset</option>
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114 <option value="paired_collection">Paired Collection</option>
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115 </param>
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116 <when value="single">
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117 <param name="fastq_input1" type="data" format="fastq,fastq.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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118 </when>
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119 <when value="paired_collection">
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120 <param name="fastq_input" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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121 </when>
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122 </conditional>
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iuc
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123 <param name="module" type="select" label="Select analysis module">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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124 <option value="FLU" selected="true">FLU</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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125 <option value="FLU-utr">FLU-utr</option>
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iuc
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126 <option value="FLU-pacbio">FLU-pacbio</option>
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127 </param>
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iuc
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128 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs">
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129 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option>
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130 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option>
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131 </param>
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132 <conditional name="advanced_config">
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133 <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in IRMA's default configuration file.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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134 <option value="no">No, use defaults for advanced settings</option>
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135 <option value="yes">Yes</option>
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136 </param>
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iuc
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diff changeset
137 <when value="no" />
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iuc
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138 <when value="yes">
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139 <conditional name="reference">
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iuc
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140 <param name="customize" type="select" label="Customize Reference Settings" help="Choosing Yes here, lets you overwrite reference settings.">
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iuc
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141 <option value="no">No, use defaults for reference settings</option>
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142 <option value="yes">Yes</option>
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diff changeset
143 </param>
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144 <when value="no" />
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145 <when value="yes">
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146 <param name="SKIP_E" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Skip reference elongation" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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147 </when>
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148 </conditional>
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149
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150 <conditional name="read_gathering">
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151 <param name="customize" type="select" label="Customize settings to read gathering" help="Choosing Yes here, lets you overwrite read gathering settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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152 <option value="no">No, use defaults for read gathering settings</option>
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153 <option value="yes">Yes</option>
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154 </param>
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155 <when value="no" />
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156 <when value="yes">
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157 <param name="MAX_ROUNDS" type="integer" min="1" max="20" value="5" label="Maximal rounds of read gathering"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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158 <param name="USE_MEDIAN" type="select" label="Use median or average for read gathering">
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159 <option value="0">Average</option>
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160 <option value="1" selected="true">Median</option>
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161 </param>
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162 <param name="QUAL_THRESHOLD" type="integer" min="0" value="30" label="Minimum read statistic to keep (Phred)"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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163 <param name="MIN_LEN" type="integer" min="0" max="1000" value="125" label="Minimum read length to keep (bp)" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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164 <param name="INCL_CHIM" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Include chimera? Transposase adapter - clips 5' of the adapter on the forward strand and 3' on the reverse strand. applicable to NextTera pair-end reads" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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165 <param name="ADAPTER" type="text" value="AGATGTGTATAAGAGACAG" label="Adapter sequence">
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166 <validator type="regex">[CAGT]+</validator>
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167 </param>
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168 <param name="ENFORCE_CLIPPED_LENGTH" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Reads are filtered for minimum length post adapter trimming" />
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169
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170 <param name="MERGE_SECONDARY" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Merge secondary data after the first round to the unmatched pool. Useful if co-infections are not expected." />
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171
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172 <param name="RESIDUAL_ASSEMBLY_FACTOR" type="integer" min="0" max="100" value="0" label="The ratio of match read patterns to altmatch is measured, and if its less than factor, residual assembly is performed. Set 0 for off."/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
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173 </when>
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174 </conditional>
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175 <conditional name="match_step">
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176 <param name="customize" type="select" label="Customize settings regarding the match step" help="Choosing Yes here, lets you overwrite match step settings.">
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177 <option value="no">No, use defaults for match step settings</option>
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178 <option value="yes">Yes</option>
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179 </param>
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180 <when value="no" />
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181 <when value="yes">
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182 <param name="MIN_RP" type="integer" min="0" value="15" label="Minimum read pattern count to continue"/>
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183 <param name="MIN_RC" type="integer" min="0" value="15" label="Minimum read count to continue"/>
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184 <param name="MIN_BLAT_MATCH" type="integer" min="0" value="0" label="Minimum read pattern count to continue"/>
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185 </when>
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186 </conditional>
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187 <conditional name="sort_step">
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188 <param name="customize" type="select" label="Customize settings regarding the sort step" help="Choosing Yes here, lets you overwrite sort step settings.">
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189 <option value="no">No, use defaults for sort step settings</option>
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190 <option value="yes">Yes</option>
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191 </param>
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192 <when value="no" />
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193 <when value="yes">
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194 <param name="SORT_PROG" type="select" label="Select program used for sorting">
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195 <option value="LABEL">LABEL</option>
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196 <option value="BLAT" selected="true">BLAT</option>
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197 </param>
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198 </when>
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199 </conditional>
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200 <conditional name="align_step">
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201 <param name="customize" type="select" label="Customize settings regarding the alignment step" help="Choosing Yes here, lets you overwrite align step settings.">
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202 <option value="no">No, use defaults for align step settings</option>
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203 <option value="yes">Yes</option>
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204 </param>
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205 <when value="no" />
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206 <when value="yes">
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207 <param name="ALIGN_PROG" type="select" label="Select program used for alignment">
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208 <option value="BLAT">BLAT</option>
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209 <option value="SAM" selected="true">SAM</option>
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210 </param>
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211 <param name="DEL_TYPE" type="select" label="How to handle deletions in rough alignment">
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212 <option value="" selected="true">Default</option>
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213 <option value="NNN">NNN</option>
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214 <option value="REF">REF</option>
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215 <option value="DEL" >DEL</option>
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216 </param>
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217 </when>
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218 </conditional>
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219 <conditional name="assembly">
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220 <param name="customize" type="select" label="Customize settings regarding the assembly" help="Choosing Yes here, lets you overwrite assembly settings.">
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221 <option value="no">No, use defaults for assembly settings</option>
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222 <option value="yes">Yes</option>
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223 </param>
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224 <when value="no" />
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225 <when value="yes">
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226 <param name="MAX_ITER_ASSEM" type="integer" min="1" value="5" label="Maximal assembly iteration"/>
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227 <!-- true and false values are inverted for the next param because we're asking the opposite question of what we need to configure -->
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228 <param name="NO_MERGE" type="boolean" falsevalue="1" truevalue="0" checked="true" label="Merge read pairs?" help="Merging read pairs after final assembly provides error detection and correction." />
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229 <param name="INS_T" type="float" min="0" max="1" value="0.25" label="The minimum frequency threshold for insertion refinement"/>
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230 <param name="DEL_T" type="float" min="0" max="1" value="0.6" label="The minimum frequency threshold for deletion refinement"/>
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231 <param name="INS_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for insertion refinement"/>
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232 <param name="DEL_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for deletion refinement"/>
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233 <param name="SILENCE_COMPLEX_INDELS" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Silences reads with complex indels (having 4 indels with at least one greater than 9)" />
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234 <param name="MIN_AMBIG" type="float" min="0" max="1" value="0.25" label="The minimum called SNV frequency for mixed base in amended consensus folder"/>
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235 <param name="SSW_M" type="integer" min="1" value="2" label="The smith-waterman match score"/>
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236 <param name="SSW_X" type="integer" min="1" value="5" label="The smith-waterman mismatch penalty"/>
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237 <param name="SSW_O" type="integer" min="1" value="10" label="The smith-waterman gap open penalty"/>
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238 <param name="SSW_E" type="integer" min="1" value="1" label="The smith-waterman gap extension penalty"/>
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239 <param name="ALIGN_AMENDED" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Do global alignment of the amended consensus to the HMM profile" />
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240 </when>
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241 </conditional>
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242 <conditional name="variant_calling">
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243 <param name="customize" type="select" label="Customize settings regarding the variant calling" help="Choosing Yes here, lets you overwrite variant calling settings.">
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244 <option value="no">No, use defaults for variant calling settings</option>
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245 <option value="yes">Yes</option>
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246 </param>
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247 <when value="no" />
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248 <when value="yes">
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249 <param name="AUTO_F" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Automatically adjust frequency threshold" />
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250 <param name="MIN_FI" type="float" min="0" max="1" value="0.005" label="The minimum insertion variant frequency"/>
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251 <param name="MIN_FD" type="float" min="0" max="1" value="0.005" label="The minimum deletion variant frequency"/>
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252 <param name="MIN_F" type="float" min="0" max="1" value="0.008" label="The minimum frequency for single nucleotide variants"/>
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253 <param name="MIN_C" type="integer" min="1" value="2" label="The minimum count for variants"/>
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254 <param name="MIN_AQ" type="integer" min="1" value="24" label="The minimum average variant quality (does not apply to deletions)"/>
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255 <param name="MIN_TCC" type="integer" min="1" value="100" label="The minimum non-ambiguous column coverage"/>
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256 <param name="MIN_CONF" type="float" min="0" max="1" value="0.80" label="The minimum confidence"/>
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257 <param name="SIG_LEVEL" type="select" label="The significance test level for variant calling">
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258 <option value="0.999" selected="true">99.9%</option>
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259 <option value="0.99" >99%</option>
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260 <option value="0.95" >95%</option>
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261 <option value="0.90" >90%</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
262 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
263 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
264 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
265 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
266 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
267 </inputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
268 <outputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
269 <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
270 <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
271 <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
272 <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
273 <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
274 <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
275 <data name="NA" format="fasta" from_work_dir="resultDir/A_NA.fasta" label="NA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
276 <data name="MP" format="fasta" from_work_dir="resultDir/A_MP.fasta" label="MP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
277 <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
278 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
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279 <!-- optional outputs-->
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
280 <collection name="bam_collection" type="list" label="Alignment files (bam)">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
281 <filter>optional_outputs and 'bam' in optional_outputs</filter>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
282 <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
283 <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
284 <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
285 <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
286 <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
287 <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
288 <data name="MP" format="bam" from_work_dir="resultDir/A_MP.bam" label="MP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
289 <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
290 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
291 <collection name="vcf_collection" type="list" label="Variant calling files (VCF)">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
292 <filter>optional_outputs and 'vcf' in optional_outputs</filter>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
293 <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
294 <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
295 <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
296 <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
297 <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
298 <data name="NA" format="vcf" from_work_dir="resultDir/A_NA.vcf" label="NA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
299 <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
300 <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
301 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
302 </outputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
303 <tests>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
304 <test expect_num_outputs="27">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
305 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
306 <param name="fastq_input1" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
307 <param name="input_type" value="single" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
308 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
309 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
310 <param name="customize" value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
311 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
312 <param name="module" value="FLU-utr" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
313 <param name="optional_outputs" value="vcf,bam"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
314 <output_collection name="consensus_collection" type="list">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
315 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
316 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
317 <has_n_lines n="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
318 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
319 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
320 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
321 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
322 <test expect_num_outputs="18">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
323 <param name="module" value="FLU"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
324 <param name="optional_outputs" value="bam"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
325 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
326 <param name="input_type" value="paired_collection"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
327 <param name="fastq_input">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
328 <collection type="paired">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
329 <element name="forward" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
330 <element name="reverse" value="test_reads_copy.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
331 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
332 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
333 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
334 <output_collection name="consensus_collection" type="list" count="8">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
335 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
336 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
337 <has_n_lines n="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
338 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
339 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
340 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
341 <output_collection name="bam_collection" type="list" count="8" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
342 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
343 <test expect_num_outputs="9">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
344 <param name="module" value="FLU-utr"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
345 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
346 <param name="input_type" value="paired_collection"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
347 <param name="fastq_input">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
348 <collection type="paired">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
349 <element name="forward" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
350 <element name="reverse" value="test_reads_copy.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
351 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
352 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
353 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
354 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
355 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
356 <conditional name="reference">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
357 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
358 <param name="SKIP_E" value="0"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
359 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
360 <conditional name="read_gathering">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
361 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
362 <param name="MAX_ROUNDS" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
363 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
364 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
365 <output_collection name="consensus_collection" type="list" count="8">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
366 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
367 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
368 <has_n_lines n="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
369 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
370 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
371 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
372 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
373 <test expect_num_outputs="27">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
374 <param name="module" value="FLU"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
375 <param name="optional_outputs" value="bam,vcf"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
376 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
377 <param name="input_type" value="paired_collection"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
378 <param name="fastq_input">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
379 <collection type="paired">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
380 <element name="forward" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
381 <element name="reverse" value="test_reads_copy.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
382 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
383 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
384 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
385 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
386 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
387 <conditional name="reference">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
388 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
389 <param name="SKIP_E" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
390 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
391 <conditional name="read_gathering">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
392 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
393 <param name="MAX_ROUNDS" value="3"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
394 <param name="USE_MEDIAN" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
395 <param name="QUAL_THRESHOLD" value="30"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
396 <param name="MIN_LEN" value="125"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
397 <param name="INCL_CHIM" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
398 <param name="ADAPTER" value="AGATGTGTATAAGAGACAG"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
399 <param name="ENFORCE_CLIPPED_LENGTH" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
400 <param name="MERGE_SECONDARY" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
401 <param name="RESIDUAL_ASSEMBLY_FACTOR" value="0"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
402 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
403 <conditional name="match_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
404 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
405 <param name="MIN_RP" value="15"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
406 <param name="MIN_RC" value="15"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
407 <param name="MIN_BLAT_MATCH" value="0"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
408 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
409 <conditional name="sort_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
410 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
411 <param name="SORT_PROG" value="LABEL"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
412 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
413 <conditional name="align_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
414 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
415 <param name="ALIGN_PROG" value="SAM"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
416 <param name="DEL_TYPE" value=""/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
417 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
418 <conditional name="assembly">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
419 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
420 <param name="MAX_ITER_ASSEM" value="5"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
421 <param name="NO_MERGE" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
422 <param name="INS_T" value="0.25"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
423 <param name="DEL_T" value="0.6"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
424 <param name="INS_T_DEPTH" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
425 <param name="DEL_T_DEPTH" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
426 <param name="SILENCE_COMPLEX_INDELS" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
427 <param name="MIN_AMBIG" value="0.25"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
428 <param name="SSW_M" value="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
429 <param name="SSW_X" value="5"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
430 <param name="SSW_O" value="10"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
431 <param name="SSW_E" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
432 <param name="ALIGN_AMENDED" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
433 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
434 <conditional name="variant_calling">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
435 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
436 <param name="AUTO_F" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
437 <param name="MIN_FI" value="0.005"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
438 <param name="MIN_FD" value="0.005"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
439 <param name="MIN_F" value="0.008"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
440 <param name="MIN_C" value="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
441 <param name="MIN_AQ" value="24"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
iuc
parents:
diff changeset
442 <param name="MIN_TCC" value="100"/>
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443 <param name="MIN_CONF" value="0.80"/>
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444 <param name="SIG_LEVEL" value="0.999"/>
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445 </conditional>
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446 </conditional>
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447 <output_collection name="consensus_collection" type="list" count="8">
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448 <element name="HA">
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449 <assert_contents>
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450 <has_n_lines n="2"/>
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451 </assert_contents>
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452 </element>
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453 </output_collection>
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454 <output_collection name="bam_collection" type="list" count="8" />
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455 <output_collection name="vcf_collection" type="list" count="8" />
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456 </test>
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457 </tests>
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458 <help><![CDATA[
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459 .. class:: infomark
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460
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461 **What it does**
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462
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463 IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses.
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464 These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.
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465 IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this galaxy wrapper currently only supports influenza modules.
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466
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467 **Inputs**
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468
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469 Specify the module and provide your read data.
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470
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471 **Outputs**
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472
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473 The default output of the tool is a collection of consensus sequences in FASTA format.
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474
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475 Optionally, collections of read mapping and variant calling results can be produced as additional outputs.
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476
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477 **Settings**
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478
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479 IRMA provides carefully chosen default settings for its different analysis modes.
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480 Advanced(!) users have the option to override these through the advanced config section.
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481
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482 .. class:: Warning mark
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483
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484 By enabling any section of the advanced configuration options you will override the default settings for *all* parameters in that section, and the default values of a section may not be IRMA's defaults for the selected module, but reflect IRMA's global defaults.
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485
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486 https://wonder.cdc.gov/amd/flu/irma/configuration.html provides more information about configuration parameters.
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487 ]]></help>
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488 <citations>
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489 <citation type="doi">10.1186/s12864-016-3030-6</citation>
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490 </citations>
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491 </tool>