Mercurial > repos > lparsons > cutadapt

annotate cutadapt.xml @ 32:5915ea1ec9b1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d8c2d0e1ce530d9cceb06cbd516296876926f0dd
author iuc
date Wed, 22 Jun 2022 07:11:38 +0000
parents c5e2e5902201
children 135b80fb1ac2
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44e2cc14f75b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7cca91ac13859592f44b2f16d3aa70c28709af8d"
iuc
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1 <tool id="cutadapt" name="Cutadapt" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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2 <description>Remove adapter sequences from FASTQ/FASTA</description>
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iuc
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3 <macros>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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4 <import>macros.xml</import>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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5 </macros>
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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6 <expand macro='edam_ontology' />
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c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
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7 <expand macro='xrefs'/>
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iuc
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8 <expand macro='requirements' />
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
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9 <version_command>cutadapt --version</version_command>
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
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8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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11 <command detect_errors="exit_code"><![CDATA[
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iuc
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12 ## Link in the input and output files, so Cutadapt can tell their type
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8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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14 #import re
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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15 #set read1 = "input_f"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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16 #set read2 = "input_r"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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17 #set paired = False
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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18 #set library_type = str($library.type)
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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19 #if $library_type == 'paired':
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iuc
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20 #set paired = True
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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21 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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22 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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23 #set input_1 = $library.input_1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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24 #set input_2 = $library.input_2
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iuc
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25 #else if $library_type == 'paired_collection'
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iuc
parents: 23
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26 #set paired = True
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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27 #set input_1 = $library.input_1.forward
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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28 #set input_2 = $library.input_1.reverse
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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29 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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30 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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31 #else
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32 #set input_1 = $library.input_1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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33 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
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34 #end if
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36 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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37 #set ext = ".fq.gz"
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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38 #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
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39 #set ext = ".fq.bz2"
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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40 #else if $input_1.is_of_type('fasta'):
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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41 #set ext = ".fa"
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42 #else:
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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43 #set ext = ".fq"
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44 #end if
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
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45 #set read1 = $read1 + $ext
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46 #set out1 = "out1" + $ext
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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47 #set rest_output = "rest_output" + $ext
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
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48 #set wild_output = "wild_output" + $ext
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iuc
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49 #set too_short_output = "too_short_output" + $ext
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50 #set too_long_output = "too_long_output" + $ext
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51 #set untrimmed_output = "untrimmed_output" + $ext
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52 ln -f -s '${input_1}' '$read1' &&
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53
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54 #if $paired:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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55 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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56 #set ext2 = ".fq.gz"
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iuc
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57 #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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58 #set ext2 = ".fq.gz"
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59 #else if $input_2.is_of_type('fasta'):
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60 #set ext2 = ".fa"
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61 #else:
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62 #set ext2 = ".fq"
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63 #end if
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64 #set read2 = $read2 + $ext2
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iuc
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65 #set out2 = "out2" + $ext2
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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66 #set too_short_paired_output = "too_short_paired_output" + $ext2
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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67 #set too_long_paired_output = "too_long_paired_output" + $ext2
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
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68 #set untrimmed_paired_output = "untrimmed_paired_output" + $ext2
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69 ln -f -s '${input_2}' '$read2' &&
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70 #end if
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71
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72 ## Run Cutadapt
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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73
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74 #if 'multiple_output' in $output_selector:
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75 mkdir split &&
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76 #end if
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77
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78 cutadapt
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79
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80 -j=\${GALAXY_SLOTS:-4}
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81
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82 #if 'json_stats' in $output_selector:
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83 --json stats.json
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84 #end if
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85
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86 #if str( $library.type ) == "single":
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87 @read1_options@
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iuc
parents: 23
diff changeset
88 #if 'multiple_output' in $output_selector:
18
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
89 --output='split/{name}.${input_1.ext}'
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
90 #else:
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
91 --output='$out1'
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
92 #end if
13
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iuc
parents: 12
diff changeset
93 #else:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
94 @read1_options@
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
95 @read2_options@
29
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iuc
parents: 28
diff changeset
96 --output='$out1'
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
97 --paired-output='$out2'
13
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iuc
parents: 12
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98 #end if
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
99
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
100 --error-rate=$adapter_options.error_rate
24
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iuc
parents: 23
diff changeset
101 --times=$adapter_options.times
13
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iuc
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diff changeset
102 --overlap=$adapter_options.overlap
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
103 $adapter_options.no_indels
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
104 $adapter_options.match_read_wildcards
24
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iuc
parents: 23
diff changeset
105 --action=$adapter_options.action
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
106 $adapter_options.revcomp
11
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iuc
parents: 10
diff changeset
107
24
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iuc
parents: 23
diff changeset
108 $filter_options.discard_trimmed
13
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iuc
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109 $filter_options.discard_untrimmed
24
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iuc
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diff changeset
110
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
111 #if str($filter_options.minimum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True':
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
112 --minimum-length=$filter_options.minimum_length:$filter_options.length_R2_options.R2_minimum
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
113 #else if str($filter_options.minimum_length):
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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114 --minimum-length=$filter_options.minimum_length
13
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iuc
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115 #end if
24
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iuc
parents: 23
diff changeset
116 #if str($filter_options.maximum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True':
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
117 --maximum-length=$filter_options.maximum_length:$filter_options.length_R2_options.R2_maximum
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
118 #else if str($filter_options.maximum_length):
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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119 --maximum-length=$filter_options.maximum_length
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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120 #end if
22
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iuc
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diff changeset
121 #if str($filter_options.max_n):
13
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iuc
parents: 12
diff changeset
122 --max-n=$filter_options.max_n
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
123 #end if
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
124 #if str( $library.type ) != "single":
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
125 #if $filter_options.pair_filter:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
126 --pair-filter=$filter_options.pair_filter
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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127 #end if
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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128 #end if
24
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iuc
parents: 23
diff changeset
129 #if str($filter_options.max_expected_errors):
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
130 --max-expected-errors=$filter_options.max_expected_errors
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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131 #end if
28
c053d4cad713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 9ec830a98da45d5fb2f92a817c7cd0376504be90"
iuc
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132 $filter_options.discard_cassava
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
133
13
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iuc
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134 #if str($read_mod_options.quality_cutoff) != '0':
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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135 --quality-cutoff=$read_mod_options.quality_cutoff
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
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136 #end if
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
137 #if str($read_mod_options.nextseq_trim) != '0':
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
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138 --nextseq-trim=$read_mod_options.nextseq_trim
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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139 #end if
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
140 $read_mod_options.trim_n
28
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iuc
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141 #if $read_mod_options.strip_suffix != ''
c053d4cad713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 9ec830a98da45d5fb2f92a817c7cd0376504be90"
iuc
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diff changeset
142 --strip-suffix $read_mod_options.strip_suffix
c053d4cad713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 9ec830a98da45d5fb2f92a817c7cd0376504be90"
iuc
parents: 27
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143 #end if
24
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iuc
parents: 23
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144 #if str($read_mod_options.shorten_options.shorten_values) == 'True':
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
145 #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
146 --length=$read_mod_options.shorten_options.length
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
147 #else
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
148 --length=-$read_mod_options.shorten_options.length
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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149 #end if
13
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150 #end if
24
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iuc
parents: 23
diff changeset
151 #if str($read_mod_options.length_tag) != '':
22
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iuc
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152 --length-tag='$read_mod_options.length_tag'
13
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iuc
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153 #end if
24
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iuc
parents: 23
diff changeset
154 #if str($read_mod_options.rename) != '':
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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155 --rename='$read_mod_options.rename'
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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156 #end if
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
157 $read_mod_options.zero_cap
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
158
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
159
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
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160 '${read1}'
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
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161 #if $paired:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
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162 '${read2}'
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
163 #if $library.r2.quality_cutoff2:
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
164 -Q=$library.r2.quality_cutoff2
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
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165 #end if
13
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iuc
parents: 12
diff changeset
166 #end if
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
167
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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168 #if 'report' in $output_selector:
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
169 > report.txt
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
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170 #end if
11
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iuc
parents: 10
diff changeset
171 ]]></command>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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172 <inputs>
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lparsons
parents: 5
diff changeset
173
11
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iuc
parents: 10
diff changeset
174 <!-- Reads -->
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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175 <conditional name="library">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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176 <param name="type" type="select" label="Single-end or Paired-end reads?">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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177 <option value="single">Single-end</option>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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178 <option value="paired">Paired-end</option>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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179 <option value="paired_collection">Paired-end Collection</option>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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180 </param>
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181
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182 <when value="single">
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183 <param name="input_1" format="@FASTQ_TYPES@" type="data" label="FASTQ/A file" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
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184 <expand macro="single_end_options" />
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185 </when>
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186
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187 <when value="paired">
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188 <param name="input_1" format="@FASTQ_TYPES@" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
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189 <param name="input_2" format="@FASTQ_TYPES@" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
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190 <expand macro="paired_end_options" />
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191 </when>
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192
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193 <when value="paired_collection">
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194 <param name="input_1" format="@FASTQ_TYPES@" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
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195 <expand macro="paired_end_options" />
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196 </when>
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197
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198 </conditional>
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199
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200 <!-- Adapter Options -->
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201 <section name="adapter_options" title="Adapter Options">
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202 <param name="action" type="select" label="What to do if a match is found">
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203 <option value="trim" selected="True">Trim: trim adapter and upstream or downstream sequence</option>
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204 <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
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205 <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
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206 <option value="lowercase">Lowercase: convert to lowercase</option>
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207 <option value="none">None: leave unchanged</option>
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208 </param>
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209 <param name="internal" type="select" label="Disallow internal adaptor ocurrences" help="The non-internal 5’ and 3’ adapter types disallow internal occurrences of the adapter sequence. The adapter must always be at one of the ends of the read, but partial occurrences are also ok.">
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210 <option value="X">Enabled</option>
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211 <option value="" selected="True">Disabled</option>
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212 </param>
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213 <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
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214 <param argument="--no-indels" type="boolean" value="False" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
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215 <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
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216 <param argument="--overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
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217 <param name="match_read_wildcards" type="select" label="Match wildcards" help="Allow 'N's as matches. Default: in the adapters but not in the reads">
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218 <option value=" " selected="True">In the adapters but not in the reads</option>
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219 <option value="--match-read-wildcards">In the adapters and in the reads</option>
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220 <option value="--no-match-adapter-wildcards">Nowhere</option>
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221 </param>
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222 <param argument="--revcomp" type="boolean" value="False" truevalue="--revcomp" falsevalue="" label="Look for adapters in the reverse complement" help="Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. Default: check only read." />
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223 </section>
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224
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225 <!-- Filter Options -->
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226 <section name="filter_options" title="Filter Options">
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227 <param argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
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228 <param argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
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229 <param argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length (R1)" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded." />
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230 <param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length (R1)" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded." />
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231 <conditional name="length_R2_options">
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232 <param name="length_R2_status" type="select" label="Specify a minimum/maximum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum/maximum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
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233 <option value="True">Enabled</option>
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234 <option value="False" selected="True">Disabled</option>
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235 </param>
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236 <when value="True">
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237 <param name="R2_minimum" type="integer" min="0" value="" optional="True" label="Minimum length (R2)" />
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238 <param name="R2_maximum" type="integer" min="0" value="" optional="True" label="Maximum length (R2)" />
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239 </when>
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240 <when value="False">
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241 </when>
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242 </conditional>
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243 <param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
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244 <param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
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245 <option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
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246 <option value="both">Both: filtering criteria must apply to both reads in order for a read pair to be discarded. </option>
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247 <option value="first">First: will make a decision about the read pair by inspecting whether the filtering criterion applies to the first read, ignoring the second read.</option>
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248
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249 </param>
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250 <param argument="--max-expected-errors" type="integer" min="0" optional="True" value="" label="Max expected errors" help="Discard reads whose expected number of errors (computed from quality values) exceeds this value." />
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251 <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
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252 </section>
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253
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254 <!-- Read Modification Options -->
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255 <section name="read_mod_options" title="Read Modification Options">
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256 <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads for paired-end data, unless a separate value for the second read is specified. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
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257 <sanitizer>
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258 <valid initial="string.digits"><add value="," /></valid>
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259 </sanitizer>
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260 <validator type="regex">[0-9,]+</validator>
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261 </param>
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262 <param argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
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263 <param argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
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264 <param argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
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265 <conditional name="shorten_options">
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266 <param name="shorten_values" type="select" label="Shortening reads to a fixed length" help="If you want to remove a fixed number of bases from each read, use the –cut option instead.">
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267 <option value="True">Enabled</option>
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268 <option value="False" selected="True">Disabled</option>
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269 </param>
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270 <when value="True">
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271 <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
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272 <param name="shorten_end" type="select" label="End at which to apply the slice">
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273 <option value="3prime">3' ends</option>
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274 <option value="5prime">5' ends</option>
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275 </param>
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276 </when>
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277 <when value="False">
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278 </when>
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279 </conditional>
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280 <param argument="--length-tag" label="Length tag" type="text" optional="True" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." >
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281 <sanitizer invalid_char="">
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282 <valid initial="string.letters,string.digits">
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283 <add value="/" />
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284 <add value="+" />
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285 <add value="-" />
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286 <add value="=" />
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287 <add value=" " />
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288 <add value="_" />
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289 </valid>
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290 </sanitizer>
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291 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
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292 </param>
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293 <param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
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294 <sanitizer invalid_char="">
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295 <valid initial="string.letters,string.digits">
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296 <add value="{" />
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297 <add value="}" />
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298 <add value="_" />
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299 <add value="=" />
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300 <add value=" " />
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301 </valid>
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302 </sanitizer>
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303 <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
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304 </param>
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305 <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
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306 </section>
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307
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308 <!-- Output Options -->
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309 <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Outputs selector">
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310 <option value="report">Report: Cutadapt's per-adapter statistics. You can use this file with MultiQC.</option>
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311 <option value="info_file">Info file: write information about each read and its adapter matches.</option>
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312 <option value="rest_file">Rest of read: when the adapter matches in the middle of a read, write the rest (after the adapter).</option>
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313 <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
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314 <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option>
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315 <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
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316 <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option>
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317 <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option>
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318 <option value="json_stats">Statistics in JSON format</option>
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319 </param>
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320 </inputs>
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321
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322 <outputs>
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323 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
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324 <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter>
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325 <expand macro="inherit_format_1" />
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326 </data>
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327
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328 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
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329 <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter>
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330 <expand macro="inherit_format_2" />
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331 </data>
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332
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333 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
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334 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
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335 <data name="forward" from_work_dir="out1.fq*" />
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336 <data name="reverse" from_work_dir="out2.fq*" />
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337 </collection>
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338
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339 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
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340 <filter>output_selector and 'report' in output_selector</filter>
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341 </data>
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342 <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
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343 <filter>output_selector and 'info_file' in output_selector</filter>
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344 </data>
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345
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346 <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
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347 <filter>output_selector and 'rest_file' in output_selector</filter>
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348 <expand macro="inherit_format_1" />
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lparsons
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349 </data>
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350
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351 <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
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352 <filter>output_selector and 'wildcard_file' in output_selector</filter>
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lparsons
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353 </data>
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354
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355 <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
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356 <filter>output_selector and 'untrimmed_file' in output_selector</filter>
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357 <expand macro="inherit_format_1" />
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lparsons
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358 </data>
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359 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
24
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iuc
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360 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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361 <filter>output_selector and 'untrimmed_file' in output_selector </filter>
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362 <expand macro="inherit_format_2" />
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iuc
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363 </data>
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364
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iuc
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diff changeset
365 <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
24
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iuc
parents: 23
diff changeset
366 <filter>output_selector and 'too_short_file' in output_selector</filter>
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iuc
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367 <expand macro="inherit_format_1" />
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lparsons
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368 </data>
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diff changeset
369 <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
24
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iuc
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diff changeset
370 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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371 <filter>output_selector and 'too_short_file' in output_selector</filter>
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372 <expand macro="inherit_format_2" />
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lparsons
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373 </data>
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diff changeset
374 <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
24
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iuc
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diff changeset
375 <filter>output_selector and 'too_long_file' in output_selector</filter>
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diff changeset
376 <expand macro="inherit_format_1" />
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iuc
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diff changeset
377 </data>
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diff changeset
378 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
24
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iuc
parents: 23
diff changeset
379 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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parents: 23
diff changeset
380 <filter>output_selector and 'too_long_file' in output_selector</filter>
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iuc
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diff changeset
381 <expand macro="inherit_format_2" />
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lparsons
parents: 8
diff changeset
382 </data>
27
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iuc
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diff changeset
383 <data name="json_stats" format="json" from_work_dir="stats.json" label="${tool.name} on ${on_string}: Statistics (JSON)" >
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
384 <filter>output_selector and 'json_stats' in output_selector</filter>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
385 </data>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
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diff changeset
386 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" format="fastqsanger" >
18
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iuc
parents: 17
diff changeset
387 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
24
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iuc
parents: 23
diff changeset
388 <filter>output_selector and 'multiple_output' in output_selector</filter>
16
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iuc
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diff changeset
389 </collection>
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diff changeset
390 </outputs>
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lparsons
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diff changeset
391
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diff changeset
392 <tests>
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diff changeset
393 <!-- Ensure fastq works -->
23
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iuc
parents: 22
diff changeset
394 <test expect_num_outputs="1">
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diff changeset
395 <param name="type" value="single" />
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iuc
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diff changeset
396 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
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iuc
parents: 24
diff changeset
397 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
398 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
399 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
400 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
401 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
402 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
403 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
404 </section>
12
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iuc
parents: 11
diff changeset
405 <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
11
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iuc
parents: 10
diff changeset
406 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
407 <!-- Ensure single end fastq.gz works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
408 <test expect_num_outputs="1">
11
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iuc
parents: 10
diff changeset
409 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
410 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
411 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
412 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
413 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
414 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
415 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
416 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
417 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
418 </section>
12
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diff changeset
419 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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lparsons
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diff changeset
420 </test>
11
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iuc
parents: 10
diff changeset
421 <!-- Ensure paired end fastq.gz works -->
23
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iuc
parents: 22
diff changeset
422 <test expect_num_outputs="2">
11
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iuc
parents: 10
diff changeset
423 <param name="type" value="paired" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
424 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
425 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
426 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
427 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
428 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
429 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
430 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
431 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
432 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
433 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
434 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
435 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
436 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
437 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
438 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
439 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
440 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
441 </section>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
442 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
443 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
444 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
445 <not_has_text text="--discard-trimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
446 <not_has_text text="--discard-untrimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
447 <not_has_text text="--minimum-length"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
448 <not_has_text text="--maximum-length"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
449 <not_has_text text="--max-n"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
450 <has_text text="--pair-filter=any"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
451 </assert_command>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
452 </test>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
453 <!-- Ensure paired collection works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
454 <test expect_num_outputs="3">
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
455 <param name="type" value="paired_collection" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
456 <param name="input_1">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
457 <collection type="paired">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
458 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
459 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
460 </collection>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
461 </param>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
462 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
463 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
464 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
465 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
466 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
467 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
468 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
469 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
470 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
471 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
472 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
473 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
474 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
475 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
476 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
477 </section>
29
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
478 <output_collection name="out_pairs" type="paired" count="2">
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
479 <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz">
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
480 <assert_contents>
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
481 <has_size value="12000" delta="2000" />
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
482 </assert_contents>
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
483 </element>
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
484 <element name="reverse" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz">
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
485 <assert_contents>
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
486 <has_size value="12000" delta="2000" />
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
487 </assert_contents>
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
488 </element>
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
489 </output_collection>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
490 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
491 <!-- Ensure built-in adapters work -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
492 <test expect_num_outputs="1">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
493 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
494 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
495 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
496 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
497 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
498 <param name="adapter_source_list" value="builtin"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
499 <param name="adapter" value="TGTAGGCC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
500 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
501 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
502 </section>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
503 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
504 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
505 <!-- Ensure discard file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
506 <test expect_num_outputs="1">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
507 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
508 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
509 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
510 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
511 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
512 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
513 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
514 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
515 </section>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
516 <section name="filter_options">
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
517 <param name="discard_trimmed" value="True"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
518 </section>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
519 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
520 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
521 <has_text text="--discard-trimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
522 </assert_command>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
523 </test>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
524 <!-- Ensure rest file output works, test json output -->
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
525 <test expect_num_outputs="3">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
526 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
527 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
528 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
529 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
530 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
531 <param name="adapter" value="AAAGATG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
532 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
533 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
534 </section>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
535 <param name="output_selector" value="rest_file,json_stats"/>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
536 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
32
5915ea1ec9b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d8c2d0e1ce530d9cceb06cbd516296876926f0dd
iuc
parents: 30
diff changeset
537 <!--allow for differing cutadapt and python version as well as two lines containing the number of cores -->
5915ea1ec9b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d8c2d0e1ce530d9cceb06cbd516296876926f0dd
iuc
parents: 30
diff changeset
538 <output name="json_stats" file="cutadapt_rest.json" ftype="json" lines_diff="8"/>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
539 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
540 </test>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
541 <!-- Ensure nextseq-trim option works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
542 <test expect_num_outputs="1">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
543 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
544 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
545 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
546 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
547 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
548 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
549 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
550 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
551 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
552 </section>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
553 <param name="nextseq_trim" value="20" />
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
554 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
555 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
556 <!-- Ensure Report and Info file output work -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
557 <test expect_num_outputs="3">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
558 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
559 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
560 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
561 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
562 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
563 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
564 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
565 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
566 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
567 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
568 <param name="output_selector" value="report,info_file" />
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
569 <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
570 <output name="report">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
571 <assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
572 <has_text text="Summary"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
573 </assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
574 </output>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
575 <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
576 </test>
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
577
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
578
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
579 <test expect_num_outputs="1">
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
580 <conditional name="library">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
581 <param name="type" value="single" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
582 <param name="input_1" ftype="fastq" value="cutadapt_in_split.fastq" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
583 <section name="r1" >
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
584 <repeat name="front_adapters">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
585 <conditional name="front_adapter_source">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
586 <param name="front_adapter_source_list" value="user"/>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
587 <param name="front_adapter_name" value="A1" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
588 <param name="front_adapter" value="^GTCGGTAA" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
589 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
590 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
591 <repeat name="front_adapters">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
592 <conditional name="front_adapter_source">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
593 <param name="front_adapter_source_list" value="user"/>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
594 <param name="front_adapter_name" value="A2" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
595 <param name="front_adapter" value="^AGGTCACT" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
596 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
597 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
598 </section>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
599 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
600 <param name="output_selector" value="multiple_output" />
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
601 <output_collection name="split_output" type="list" count="3">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
602 <element name="A1" value="A1.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
603 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
604 <element name="A2" value="A2.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
605 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
606 <element name="unknown" value="unknown.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
607 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
608 </output_collection>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
609 </test>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
610
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
611 <test expect_num_outputs="1">
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
612 <conditional name="library">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
613 <param name="type" value="single" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
614 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
615 <section name="r1" >
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
616 <repeat name="front_adapters">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
617 <conditional name="front_adapter_source">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
618 <param name="front_adapter_source_list" value="file"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
619 <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
620 </conditional>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
621 </repeat>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
622 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
623 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
624 <param name="output_selector" value="multiple_output" />
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
625 <output_collection name="split_output" type="list" count="3">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
626 <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
627 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
628 <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
629 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
630 <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
631 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
632 </output_collection>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
633 </test>
18
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
634
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
635 <!-- Ensure untrimmed file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
636 <test expect_num_outputs="2">
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
637 <param name="type" value="single" />
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
638 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
639 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
640 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
641 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
642 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
643 <param name="adapter" value="AAAT"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
644 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
645 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
646 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
647 <param name="output_selector" value="untrimmed_file" />
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
648 <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
649 <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
650 </test>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
651 <!-- Ensure untrimmed gzip file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
652 <test expect_num_outputs="2">
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
653 <param name="type" value="single" />
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
654 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
655 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
656 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
657 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
658 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
659 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
660 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
661 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
662 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
663 <param name="output_selector" value="untrimmed_file" />
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
664 <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
665 <!--
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
666 Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
667 See discussion at https://github.com/galaxyproject/galaxy/issues/7671
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
668 `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
669 difference between level 1 compression and no compression
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
670 -->
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
671 <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
672 </test>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
673 <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
674 <test expect_num_outputs="2">
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
675 <param name="type" value="paired" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
676 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
677 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
678 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
679 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
680 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
681 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
682 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
683 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
684 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
685 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
686 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
687 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
688 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
689 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
690 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
691 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
692 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
693 </section>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
694 <section name="filter_options">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
695 <param name="discard_untrimmed" value="true"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
696 <param name="minimun_length" value="1"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
697 <param name="maximum_length" value="1000"/>
22
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 21
diff changeset
698 <param name="max_n" value="0"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
699 <param name="pair_filter" value="both"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
700 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
701 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
702 <has_text text="--discard-untrimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
703 <has_text text="--maximum-length=1000"/>
22
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 21
diff changeset
704 <has_text text="--max-n=0"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
705 <has_text text="--pair-filter=both"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
706 </assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
707 </test>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
708 <!-- Test cut option -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
709 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
710 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
711 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
712 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
713 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
714 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
715 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
716 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
717 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
718 </repeat>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
719 <param name="cut" value="5"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
720 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
721 <output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
722 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
723 <!-- Test rename options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
724 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
725 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
726 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
727 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
728 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
729 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
730 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
731 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
732 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
733 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
734 <param name="cut" value="5"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
735 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
736 <section name="read_mod_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
737 <param name="rename" value="{id} barcode={cut_prefix}"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
738 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
739 <output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
740 <assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
741 <has_text text="@prefix:1_13_1259/1 barcode=AGCCG"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
742 </assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
743 </output>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
744 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
745 <!-- Test action options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
746 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
747 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
748 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
749 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
750 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
751 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
752 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
753 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
754 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
755 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
756 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
757 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
758 <param name="action" value="retain"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
759 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
760 <output name="out1" file="cutadapt_action_retain.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
761 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
762 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
763 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
764 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
765 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
766 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
767 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
768 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
769 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
770 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
771 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
772 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
773 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
774 <param name="action" value="mask"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
775 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
776 <output name="out1" file="cutadapt_action_mask.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
777 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
778 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
779 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
780 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
781 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
782 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
783 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
784 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
785 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
786 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
787 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
788 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
789 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
790 <param name="action" value="lowercase"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
791 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
792 <output name="out1" file="cutadapt_action_lowercase.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
793 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
794 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
795 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
796 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
797 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
798 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
799 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
800 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
801 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
802 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
803 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
804 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
805 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
806 <param name="action" value="none"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
807 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
808 <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
809 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
810 <!-- Test revcomp options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
811 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
812 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
813 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
814 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
815 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
816 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
817 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
818 <param name="adapter" value="TAAACAGATTAGT"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
819 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
820 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
821 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
822 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
823 <param name="revcomp" value="true"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
824 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
825 <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
826 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
827 <!-- Test minimum lenghth paired-reads -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
828 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
829 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
830 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
831 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
832 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
833 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
834 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
835 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
836 <param name="adapter" value="ATCTGGTTCC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
837 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
838 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
839 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
840 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
841 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
842 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
843 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
844 <param name="adapter2" value="CTACAAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
845 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
846 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
847 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
848 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
849 <param name="minimum_length" value="30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
850 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
851 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
852 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
853 <param name="R2_minimum" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
854 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
855 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
856 <output name="out1" decompress="True" file="cutadapt_out1_min_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
857 <output name="out2" decompress="True" file="cutadapt_out2_min_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
858 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
859 <has_text text="--minimum-length=30:10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
860 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
861 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
862 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
863 <!-- Test maximum lenghth paired-reads -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
864 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
865 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
866 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
867 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
868 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
869 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
870 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
871 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
872 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
873 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
874 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
875 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
876 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
877 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
878 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
879 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
880 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
881 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
882 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
883 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
884 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
885 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
886 <param name="maximum_length" value="50"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
887 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
888 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
889 <param name="R2_maximum" value="30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
890 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
891 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
892 <output name="out1" decompress="True" file="cutadapt_out1_max_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
893 <output name="out2" decompress="True" file="cutadapt_out2_max_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
894 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
895 <has_text text="--maximum-length=50:30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
896 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
897 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
898 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
899 <!-- Test combination maximum and minimum length paired reads -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
900 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
901 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
902 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
903 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
904 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
905 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
906 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
907 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
908 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
909 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
910 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
911 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
912 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
913 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
914 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
915 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
916 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
917 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
918 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
919 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
920 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
921 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
922 <param name="minimum_length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
923 <param name="maximum_length" value="50"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
924 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
925 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
926 <param name="R2_maximum" value="30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
927 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
928 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
929 <output name="out1" decompress="True" file="cutadapt_out1_max_min_01.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
930 <output name="out2" decompress="True" file="cutadapt_out2_max_min_01.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
931 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
932 <has_text text="--minimum-length=10:"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
933 <has_text text="--maximum-length=50:30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
934 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
935 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
936 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
937 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
938 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
939 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
940 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
941 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
942 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
943 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
944 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
945 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
946 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
947 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
948 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
949 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
950 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
951 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
952 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
953 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
954 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
955 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
956 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
957 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
958 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
959 <param name="minimum_length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
960 <param name="maximum_length" value="50"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
961 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
962 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
963 <param name="R2_minimum" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
964 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
965 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
966 <output name="out1" decompress="True" file="cutadapt_out1_max_min_02.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
967 <output name="out2" decompress="True" file="cutadapt_out2_max_min_02.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
968 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
969 <has_text text="--minimum-length=10:10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
970 <has_text text="--maximum-length=50:"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
971 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
972 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
973 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
974 <!-- Test length options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
975 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
976 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
977 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
978 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
979 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
980 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
981 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
982 <param name="adapter" value="AGCCGCTANGACG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
983 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
984 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
985 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
986 <section name="read_mod_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
987 <conditional name="shorten_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
988 <param name="shorten_values" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
989 <param name="shorten_end" value="3prime"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
990 <param name="length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
991 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
992 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
993 <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
994 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
995 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
996 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
997 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
998 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
999 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1000 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1001 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1002 <param name="adapter" value="AGCCGCTANGACG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1003 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1004 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1005 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1006 <section name="read_mod_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1007 <conditional name="shorten_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1008 <param name="shorten_values" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1009 <param name="shorten_end" value="5prime"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1010 <param name="length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1011 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1012 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1013 <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1014 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1015 <!-- Test max expected errors options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1016 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1017 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1018 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1019 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1020 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1021 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1022 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1023 <param name="adapter" value="AGCGGCTTAGACG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1024 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1025 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1026 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1027 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1028 <param name="max_expected_errors" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1029 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1030 <output name="out1" file="cutadapt_shorten_expected_errors.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1031 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1032 <!-- Test disallow internal adaptors option -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1033 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1034 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1035 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1036 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1037 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1038 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1039 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1040 <param name="adapter" value="GAANTAGCTACCAC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1041 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1042 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1043 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1044 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1045 <param name="internal" value="X"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1046 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1047 <output name="out1" file="cutadapt_shorten_internal_adapters.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1048 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1049 <has_text text="GAANTAGCTACCACX"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1050 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1051 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1052 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1053 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1054 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1055 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1056 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1057 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1058 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1059 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1060 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1061 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1062 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1063 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1064 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1065 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1066 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1067 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1068 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1069 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1070 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1071 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1072 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1073 <param name="internal" value="X"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1074 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1075 <output name="out1" decompress="True" file="cutadapt_out1_internal_adapter.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1076 <output name="out2" decompress="True" file="cutadapt_out2_internal_adapter.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1077 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1078 <has_text text="AGATCGGAAGAGCX"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1079 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1080 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1081 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1082 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1083 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1084 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1085 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1086 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1087 <param name="adapter_source_list" value="builtin"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1088 <param name="adapter" value="TGTAGGCC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1089 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1090 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1091 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1092 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1093 <param name="internal" value="X"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1094 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1095 <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1096 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1097 <has_text text="TGTAGGCCX"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1098 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1099 </test>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1100 <!-- Ensure individual per adapter noindels parameter works -->
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1101 <test expect_num_outputs="3">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1102 <param name="type" value="paired_collection" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1103 <param name="input_1">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1104 <collection type="paired">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1105 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1106 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1107 </collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1108 </param>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1109 <section name="r1">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1110 <repeat name="adapters">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1111 <conditional name="adapter_source">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1112 <param name="adapter_source_list" value="user"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1113 <param name="adapter" value="AGATCGGAAGAGC"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1114 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1115 <param name="single_noindels" value=";noindels" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1116 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1117 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1118 <section name="r2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1119 <repeat name="adapters2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1120 <conditional name="adapter_source2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1121 <param name="adapter_source_list2" value="user"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1122 <param name="adapter2" value="AGATCGGAAGAGC"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1123 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1124 <param name="single_noindels" value=";noindels" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1125 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1126 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1127 <output_collection name="out_pairs" type="paired">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1128 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1129 <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1130 </output_collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1131 </test>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1132 <!-- Ensure specifying quality cutoff (for both reads) works -->
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1133 <test expect_num_outputs="3">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1134 <param name="type" value="paired_collection" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1135 <param name="input_1">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1136 <collection type="paired">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1137 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1138 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1139 </collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1140 </param>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1141 <param name="quality_cutoff" value="5" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1142 <section name="r1">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1143 <repeat name="adapters">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1144 <conditional name="adapter_source">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1145 <param name="adapter_source_list" value="user"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1146 <param name="adapter" value="AGATCGGAAGAGC"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1147 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1148 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1149 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1150 <section name="r2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1151 <repeat name="adapters2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1152 <conditional name="adapter_source2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1153 <param name="adapter_source_list2" value="user"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1154 <param name="adapter2" value="AGATCGGAAGAGC"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1155 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1156 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1157 <param name="quality_cutoff2" value="15,20"/>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1158 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1159 <output_collection name="out_pairs" type="paired">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1160 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1161 <element name="reverse" decompress="True" file="cutadapt_out2_cutoff.fq.gz" ftype="fastq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1162 </output_collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1163 </test>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1164 </tests>
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1165
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1166 <help><![CDATA[
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1167
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1168 .. class:: infomark
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1169
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1170 **What it does**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1171
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1172 -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1173
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1174 **Cutadapt** finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1175
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1176 Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced, such as in microRNA, or CRISPR data, or Poly-A tails that are useful for pulling out RNA from your sample but often you don’t want them to be in your reads.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1177
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1178 Cutadapt_ helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Cutadapt searches for the adapter in all reads and removes it when it finds it. Unless you use a filtering option, all reads that were present in the input file will also be present in the output file, some of them trimmed, some of them not. Even reads that were trimmed entirely (because the adapter was found in the very beginning) are output. All of this can be changed with options in the tool form above.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1179
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1180 The tool is based on the **Open Source** Cutadapt_ tool. See the complete `Cutadapt documentation`_ for additional details. If you use Cutadapt, please cite *Marcel, 2011* under **Citations** below.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1181
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1182 -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1183
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1184 **Inputs**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1185
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1186 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1187
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1188 Input files for Cutadapt need to be:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1189
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1190 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1191
19
49370cb85f0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents: 18
diff changeset
1192 To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1193
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1194 ============================================= ===================
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1195 **Option** **Sequence**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1196 --------------------------------------------- -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1197 3’ (End) Adapter ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1198 Anchored 3’ Adapter ADAPTER$
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1199
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1200 5’ (Front) Adapter ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1201 Anchored 5’ Adapter ^ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1202
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1203 5’ or 3’ (Both possible) ADAPTER
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1204
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1205 Linked Adapter - 3' (End) only ADAPTER1...ADAPTER2
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1206 Non-anchored Linked Adapter - 5' (Front) only ADAPTER1...ADAPTER2
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1207 ============================================= ===================
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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parents: 10
diff changeset
1208
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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parents: 10
diff changeset
1209 Below is an illustration of the allowed adapter locations relative to the read and depending on the adapter type:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1210
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1211 .. image:: $PATH_TO_IMAGES/adapters.svg
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1212
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1213
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1214 -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1215
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1216 *Example: Illumina TruSeq Adapters*
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1217
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1218 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1219
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1220 If you have reads containing Illumina TruSeq adapters, for example, follow these steps.
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1221
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1222
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1223 For Single-end reads as well as the first reads of Paired-end data:
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1224
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1225 **Read 1**
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1226
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1227 In the **3' (End) Adapters** option above, insert A + the “TruSeq Indexed Adapter” prefix that is common to all Indexed Adapter sequences, e.g insert:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1228
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1229 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1230
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1231
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1232 For the second reads of Paired-end data:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1233
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1234 **Read 2**
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1235
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1236 In the **3' (End) Adapters** option above, insert the reverse complement of the “TruSeq Universal Adapter”:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1237
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1238 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1239
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1240 The adapter sequences can be found in the document `Illumina TruSeq Adapters De-Mystified`_.
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1241
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1242 -----------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1243
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1244 **Outputs**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1245
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1246 -----------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1247
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1248 - Trimmed reads
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1249
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1250 Optionally, under **Output Options** you can choose to output
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1251
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1252 * Report
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1253 * Info file
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1254
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1255
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1256 **Report**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1257
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1258 Cutadapt can output per-adapter statistics if you select to output the report above.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1259
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1260 Example:
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1261
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1262 ::
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1263
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1264 This is cutadapt 3.4 with Python 3.9.2
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1265
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1266 Command line parameters: -j=1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1267 --overlap=3 --action=trim --minimum-length=30:40 --pair-filter=both --cut=0 bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1268
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1269 Processing reads on 1 core in paired-end mode ...
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1270 Finished in 0.01 s (129 µs/read; 0.46 M reads/minute).
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1271
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1272 === Summary ===
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1273
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1274 Total read pairs processed: 99
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1275 Read 1 with adapter: 2 (2.0%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1276 Read 2 with adapter: 4 (4.0%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1277 Pairs that were too short: 3 (3.0%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1278 Pairs written (passing filters): 96 (97.0%)
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1279
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1280 Total basepairs processed: 48,291 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1281 Read 1: 24,147 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1282 Read 2: 24,144 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1283 Total written (filtered): 48,171 bp (99.8%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1284 Read 1: 24,090 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1285 Read 2: 24,081 bp
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1286
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1287
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1288 **Info file**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1289
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1290 The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1291
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1292 Columns contain the following data:
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1293
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1294 * **1st**: Read name
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1295 * **2nd**: Number of errors
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1296 * **3rd**: 0-based start coordinate of the adapter match
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1297 * **4th**: 0-based end coordinate of the adapter match
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1298 * **5th**: Sequence of the read to the left of the adapter match (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1299 * **6th**: Sequence of the read that was matched to the adapter
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1300 * **7th**: Sequence of the read to the right of the adapter match (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1301 * **8th**: Name of the found adapter
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1302 * **9th**: Quality values corresponding to sequence left of the adapter match (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1303 * **10th**: Quality values corresponding to sequence matched to the adapter (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1304 * **11th**: Quality values corresponding to sequence to the right of the adapter (can be empty)
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1305
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1306 The concatenation of columns 5-7 yields the full read sequence. Column 8 identifies the found adapter. Adapters without a name are numbered starting from 1. Fields 9-11 are empty if quality values are not available. Concatenating them yields the full sequence of quality values.
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1307
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1308 If no adapter was found, the format is as follows:
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1309
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1310 #. Read name
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1311 #. The value -1
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1312 #. The read sequence
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1313 #. Quality values
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1314
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1315 When parsing the file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1316
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1317 If the --times option is used and greater than 1, each read can appear more than once in the info file. There will be one line for each found adapter, all with identical read names. Only for the first of those lines will the concatenation of columns 5-7 be identical to the original read sequence (and accordingly for columns 9-11). For subsequent lines, the shown sequence are the ones that were used in subsequent rounds of adapter trimming, that is, they get successively shorter.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1318
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1319
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1320 --------------------
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1321
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1322 **Rename Reads**
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1323
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1324 --------------------
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1325
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1326
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1327 The --rename option expects a template string such as {id} extra_info {adapter_name} as a parameter. It can contain regular text and placeholders that consist of a name enclosed in curly braces ({placeholdername}).
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1328
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1329 The read name will be set to the template string in which the placeholders are replaced with the actual values relevant for the current read.
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1330
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1331 The following placeholders are currently available for single-end reads:
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diff changeset
1332
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1333 * {header} – the full, unchanged header
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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diff changeset
1334 * {id} – the read ID, that is, the part of the header before the first whitespace
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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1335 * {comment} – the part of the header after the whitespace following the ID
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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1336 * {adapter_name} – the name of adapter that was found in this read or no_adapter if there was none adapter match. If you use --times to do multiple rounds of adapter matching, this is the name of the last found adapter.
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iuc
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diff changeset
1337 * {match_sequence} – the sequence of the read that matched the adapter (including errors). If there was no adapter match, this is set to an empty string. If you use a linked adapter, this is to the two matching strings, separated by a comma.
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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diff changeset
1338 * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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diff changeset
1339 * {cut_suffix} – the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument)
30
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diff changeset
1340 * {rc} – this is replaced with the string rc if the read was reverse complemented. This only applies when reverse complementing was requested
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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diff changeset
1341
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parents: 23
diff changeset
1342 If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1’s comment in R1 and it becomes R2’s comment in R2.
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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diff changeset
1343
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diff changeset
1344 For paired-end data, the placeholder {rn} is available (“read number”), and it is replaced with 1 in R1 and with 2 in R2.
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
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diff changeset
1345
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
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diff changeset
1346 In addition, it is possible to write a placeholder as {r1.placeholdername} or {r2.placeholdername}, which always takes the replacement value from R1 or R2, respectively.
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
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diff changeset
1347 The {r1.placeholder} and {r2.placeholder} notation is available for all placeholders except {rn} and {id} because the read ID needs to be identical for both reads.
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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diff changeset
1348
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1349 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1350
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1351 **More Information**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1352
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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1353 --------------------
9
93d58ffe39f1 Updated to version 1.6
lparsons
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diff changeset
1354
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1355 See the excellent `Cutadapt documentation`_
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1356
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1357 .. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1358 .. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1359 .. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1360
9
93d58ffe39f1 Updated to version 1.6
lparsons
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diff changeset
1361
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1362 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1363
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1364 **Galaxy Wrapper Development**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1365
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1366 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1367
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1368 Author: Lance Parsons <lparsons@princeton.edu>
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diff changeset
1369
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diff changeset
1370 ]]></help>
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diff changeset
1371 <expand macro="citations" />
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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diff changeset
1372 </tool>