Mercurial > repos > lparsons > cutadapt

annotate cutadapt.xml @ 30:c5e2e5902201 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
author iuc
date Wed, 02 Mar 2022 08:37:02 +0000
parents 48f587c13075
children 5915ea1ec9b1
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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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3 <macros>
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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"
iuc
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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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10
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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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13
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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
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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"
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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"
iuc
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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
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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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iuc
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31 #else
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iuc
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32 #set input_1 = $library.input_1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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33 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
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34 #end if
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35
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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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41 #set ext = ".fa"
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42 #else:
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43 #set ext = ".fq"
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44 #end if
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45 #set read1 = $read1 + $ext
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46 #set out1 = "out1" + $ext
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47 #set rest_output = "rest_output" + $ext
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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
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55 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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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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65 #set out2 = "out2" + $ext2
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66 #set too_short_paired_output = "too_short_paired_output" + $ext2
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67 #set too_long_paired_output = "too_long_paired_output" + $ext2
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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"/>
30
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
iuc
parents: 29
diff changeset
537 <output name="json_stats" file="cutadapt_rest.json" ftype="json" lines_diff="4"/> <!--allow for differing cutadapt and python version-->
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
538 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
539 </test>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
540 <!-- 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
541 <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
542 <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
543 <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
544 <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
545 <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
546 <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
547 <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
548 <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
549 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
550 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
551 </section>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
552 <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
553 <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
554 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
555 <!-- 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
556 <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
557 <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
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
565 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
566 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
567 <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
568 <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
569 <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
570 <assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
571 <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
572 </assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
573 </output>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
574 <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
575 </test>
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
576
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
577
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
578 <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
579 <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
580 <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
581 <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
582 <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
583 <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
584 <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
585 <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
586 <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
587 <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
588 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
589 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
590 <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
591 <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
592 <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
593 <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
594 <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
595 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
596 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
597 </section>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
598 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
599 <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
600 <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
601 <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
602 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
603 <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
604 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
605 <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
606 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
607 </output_collection>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
608 </test>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
609
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
610 <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
611 <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
612 <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
613 <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
614 <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
615 <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
616 <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
617 <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
618 <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
619 </conditional>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
620 </repeat>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
621 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
622 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
623 <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
624 <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
625 <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
626 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
627 <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
628 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
629 <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
630 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
631 </output_collection>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
632 </test>
18
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
633
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
634 <!-- 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
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 <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
642 <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
643 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
644 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
645 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
646 <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
647 <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
648 <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
649 </test>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
650 <!-- 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
651 <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
652 <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
653 <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
654 <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
655 <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
656 <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
657 <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
658 <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
659 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
660 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
661 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
662 <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
663 <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
664 <!--
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
665 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
666 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
667 `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
668 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
669 -->
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
670 <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
671 </test>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
672 <!-- 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
673 <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
674 <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
675 <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
676 <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
677 <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
678 <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
679 <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
680 <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
681 <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
682 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
683 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
684 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
685 <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
686 <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
687 <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
688 <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
689 <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
690 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
691 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
692 </section>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
693 <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
694 <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
695 <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
696 <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
697 <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
698 <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
699 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
700 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
701 <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
702 <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
703 <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
704 <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
705 </assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
706 </test>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
707 <!-- 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
708 <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
709 <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
710 <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
711 <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
712 <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
713 <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
714 <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
715 <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
716 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
717 </repeat>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
718 <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
719 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
720 <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
721 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
722 <!-- 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
723 <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
724 <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
725 <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
726 <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
727 <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
728 <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
729 <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
730 <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
731 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
732 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
733 <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
734 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
735 <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
736 <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
737 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
738 <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
739 <assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
740 <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
741 </assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
742 </output>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
743 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
744 <!-- 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
745 <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
746 <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
747 <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
748 <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
749 <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
750 <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
751 <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
752 <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
753 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
754 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
755 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
756 <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
757 <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
758 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
759 <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
760 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
761 <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
762 <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
763 <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
764 <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
765 <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
766 <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
767 <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
768 <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
769 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
770 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
771 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
772 <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
773 <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
774 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
775 <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
776 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 <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
784 <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
785 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
786 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
787 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
788 <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
789 <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
790 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
791 <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
792 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
793 <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
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 <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
801 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
802 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
803 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
804 <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
805 <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
806 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
807 <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
808 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
809 <!-- 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
810 <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
811 <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
812 <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
813 <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
814 <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
815 <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
816 <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
817 <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
818 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
819 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
820 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
821 <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
822 <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
823 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
824 <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
825 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
826 <!-- 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
827 <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
828 <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
829 <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
830 <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
831 <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
832 <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
833 <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
834 <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
835 <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
836 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
837 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
838 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
839 <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
840 <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
841 <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
842 <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
843 <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
844 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
845 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
846 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
847 <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
848 <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
849 <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
850 <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
851 <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
852 <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
853 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
854 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
855 <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
856 <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
857 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
858 <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
859 <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
860 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
861 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
862 <!-- 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
863 <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
864 <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
865 <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
866 <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
867 <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
868 <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
869 <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
870 <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
871 <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
872 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
873 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
874 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
875 <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
876 <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
877 <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
878 <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
879 <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
880 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
881 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
882 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
883 <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
884 <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
885 <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
886 <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
887 <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
888 <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
889 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
890 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
891 <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
892 <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
893 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
894 <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
895 <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
896 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
897 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
898 <!-- 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
899 <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
900 <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
901 <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
902 <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
903 <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
904 <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
905 <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
906 <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
907 <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
908 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
909 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
910 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
911 <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
912 <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
913 <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
914 <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
915 <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
916 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
917 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
918 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
919 <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
920 <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
921 <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
922 <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
923 <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
924 <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
925 <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
926 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
927 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
928 <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
929 <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
930 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
931 <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
932 <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
933 <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
934 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
935 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
936 <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
937 <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
938 <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
939 <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
940 <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
941 <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
942 <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
943 <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
944 <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
945 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
946 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
947 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
948 <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
949 <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
950 <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
951 <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
952 <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
953 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
954 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
955 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
956 <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
957 <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
958 <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
959 <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
960 <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
961 <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
962 <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
963 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
964 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
965 <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
966 <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
967 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
968 <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
969 <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
970 <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
971 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
972 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
973 <!-- 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
974 <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
975 <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
976 <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
977 <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
978 <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
979 <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
980 <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
981 <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
982 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
983 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
984 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
985 <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
986 <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
987 <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
988 <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
989 <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
990 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
991 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
992 <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
993 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
994 <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
995 <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
996 <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
997 <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
998 <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
999 <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
1000 <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
1001 <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
1002 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1003 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1004 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1005 <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
1006 <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
1007 <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
1008 <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
1009 <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
1010 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1011 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1012 <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
1013 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1014 <!-- 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
1015 <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
1016 <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
1017 <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
1018 <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
1019 <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
1020 <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
1021 <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
1022 <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
1023 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1024 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1025 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1026 <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
1027 <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
1028 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1029 <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
1030 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1031 <!-- 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
1032 <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
1033 <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
1034 <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
1035 <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
1036 <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
1037 <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
1038 <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
1039 <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
1040 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1041 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1042 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1043 <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
1044 <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
1045 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1046 <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
1047 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1048 <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
1049 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1050 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1051 <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
1052 <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
1053 <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
1054 <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
1055 <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
1056 <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
1057 <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
1058 <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
1059 <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
1060 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1061 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1062 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1063 <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
1064 <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
1065 <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
1066 <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
1067 <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
1068 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1069 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1070 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1071 <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
1072 <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
1073 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1074 <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
1075 <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
1076 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1077 <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
1078 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1079 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1080 <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
1081 <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
1082 <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
1083 <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
1084 <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
1085 <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
1086 <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
1087 <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
1088 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1089 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1090 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1091 <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
1092 <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
1093 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1094 <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
1095 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1096 <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
1097 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1098 </test>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1099 <!-- 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
1100 <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
1101 <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
1102 <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
1103 <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
1104 <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
1105 <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
1106 </collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1107 </param>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1108 <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
1109 <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
1110 <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
1111 <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
1112 <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
1113 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1114 <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
1115 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1116 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1117 <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
1118 <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
1119 <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
1120 <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
1121 <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
1122 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1123 <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
1124 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1125 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1126 <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
1127 <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
1128 <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
1129 </output_collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1130 </test>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1131 <!-- 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
1132 <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
1133 <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
1134 <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
1135 <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
1136 <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
1137 <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
1138 </collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1139 </param>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1140 <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
1141 <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
1142 <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
1143 <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
1144 <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
1145 <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
1146 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1147 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1148 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1149 <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
1150 <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
1151 <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
1152 <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
1153 <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
1154 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1155 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1156 <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
1157 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1158 <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
1159 <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
1160 <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
1161 </output_collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1162 </test>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1163 </tests>
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1164
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1165 <help><![CDATA[
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1166
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1167 .. class:: infomark
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1168
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1169 **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
1170
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 **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
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diff changeset
1174
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1175 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
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diff changeset
1176
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1177 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
1178
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1179 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
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diff changeset
1180
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 **Inputs**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1184
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1185 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1186
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1187 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
1188
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1189 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1190
19
49370cb85f0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
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diff changeset
1191 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
1192
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1193 ============================================= ===================
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1194 **Option** **Sequence**
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
1195 --------------------------------------------- -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1196 3’ (End) Adapter ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1197 Anchored 3’ Adapter ADAPTER$
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1198
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1199 5’ (Front) Adapter ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1200 Anchored 5’ Adapter ^ADAPTER
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diff changeset
1201
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iuc
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diff changeset
1202 5’ or 3’ (Both possible) ADAPTER
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1203
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1204 Linked Adapter - 3' (End) only ADAPTER1...ADAPTER2
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1205 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
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diff changeset
1206 ============================================= ===================
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diff changeset
1207
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1208 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
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diff changeset
1209
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1210 .. image:: $PATH_TO_IMAGES/adapters.svg
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1211
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1212
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1213 -------------------
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diff changeset
1214
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1215 *Example: Illumina TruSeq Adapters*
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1216
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1217 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1218
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1219 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
1220
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1221
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1222 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
1223
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1224 **Read 1**
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1225
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1226 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
1227
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1228 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1229
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1230
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1231 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
1232
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1233 **Read 2**
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1234
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1235 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
1236
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1237 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1238
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1239 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
1240
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1241 -----------
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 **Outputs**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1244
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1245 -----------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1246
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1247 - Trimmed reads
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1248
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1249 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
1250
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1251 * Report
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1252 * Info file
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1253
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1254
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1255 **Report**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1256
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1257 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
1258
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1259 Example:
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1260
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1261 ::
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 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
1264
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1265 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
1266 --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
1267
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1268 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
1269 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
1270
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1271 === Summary ===
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1272
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1273 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
1274 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
1275 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
1276 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
1277 Pairs written (passing filters): 96 (97.0%)
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1278
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1279 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
1280 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
1281 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
1282 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
1283 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
1284 Read 2: 24,081 bp
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1285
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1286
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1287 **Info file**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1288
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1289 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
1290
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1291 Columns contain the following data:
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1292
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1293 * **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
1294 * **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
1295 * **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
1296 * **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
1297 * **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
1298 * **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
1299 * **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
1300 * **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
1301 * **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
1302 * **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
1303 * **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
1304
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1305 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
1306
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1307 If no adapter was found, the format is as follows:
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1308
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1309 #. Read name
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1310 #. 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
1311 #. 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
1312 #. Quality values
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1313
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1314 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
1315
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1316 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
1317
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1318
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 **Rename Reads**
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1322
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 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
1327
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1328 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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1329
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1330 The following placeholders are currently available for single-end reads:
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1331
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1332 * {header} – the full, unchanged header
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1333 * {id} – the read ID, that is, the part of the header before the first whitespace
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1334 * {comment} – the part of the header after the whitespace following the ID
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1335 * {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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1336 * {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.
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1337 * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)
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1338 * {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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1339 * {rc} – this is replaced with the string rc if the read was reverse complemented. This only applies when reverse complementing was requested
24
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1340
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diff changeset
1341 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.
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1342
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1343 For paired-end data, the placeholder {rn} is available (“read number”), and it is replaced with 1 in R1 and with 2 in R2.
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1344
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1345 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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1346 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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1347
11
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1348 --------------------
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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1350 **More Information**
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1351
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1352 --------------------
9
93d58ffe39f1 Updated to version 1.6
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1353
11
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1354 See the excellent `Cutadapt documentation`_
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1355
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1356 .. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/
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1357 .. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html
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1358 .. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf
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1359
9
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1360
11
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1361 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1362
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1363 **Galaxy Wrapper Development**
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1364
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1365 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1366
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1367 Author: Lance Parsons <lparsons@princeton.edu>
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1368
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1369 ]]></help>
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1370 <expand macro="citations" />
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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1371 </tool>