Mercurial > repos > lparsons > cutadapt

annotate cutadapt.xml @ 35:9845c649f41b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
author iuc
date Sun, 17 Dec 2023 18:52:25 +0000
parents 135b80fb1ac2
children 64172f1c1202
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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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2 <description>Remove adapter sequences from FASTQ/FASTA</description>
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3 <macros>
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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
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5 </macros>
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6 <expand macro='edam_ontology' />
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c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
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7 <expand macro='xrefs'/>
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iuc
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8 <expand macro='requirements' />
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
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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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12 ## Link in the input and output files, so Cutadapt can tell their type
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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14 #import re
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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15 #set read1 = "input_f"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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16 #set read2 = "input_r"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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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
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19 #if $library_type == 'paired':
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20 #set paired = True
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21 #set input_1 = $library.input_1
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22 #set input_2 = $library.input_2
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23 ## Avoid the paired read input files sharing the same name, else the program still runs but
135b80fb1ac2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7143af903be8405ca77d524b343e0973304be693
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24 ## uses inaccurate results by using only 1 of 2 files.
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25 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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26 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
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27 #if read1 == read2:
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28 #set read1 = read1 + "_1"
135b80fb1ac2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7143af903be8405ca77d524b343e0973304be693
iuc
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29 #set read2 = read2 + "_2"
135b80fb1ac2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7143af903be8405ca77d524b343e0973304be693
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30 #end if
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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31 #else if $library_type == 'paired_collection'
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32 #set paired = True
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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33 #set input_1 = $library.input_1.forward
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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34 #set input_2 = $library.input_1.reverse
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35 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
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36 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
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37 #else
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38 #set input_1 = $library.input_1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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39 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
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40 #end if
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42 #if $input_1.is_of_type("fastq"):
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
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43 #set ext = ".fq"
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44 #else
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45 #set ext = ".fa"
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46 #end if
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47 #if $input_1.ext.endswith(".gz"):
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48 #set ext=ext+".gz"
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49 #elif $input_1.ext.endswith(".bz2")
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50 #set ext=ext+".bz2"
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51 #end if
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53
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54 #set read1 = $read1 + $ext
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55 #set out1 = "out1" + $ext
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56 #set rest_output = "rest_output" + $ext
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57 #set wild_output = "wild_output" + $ext
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58 #set too_short_output = "too_short_output" + $ext
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59 #set too_long_output = "too_long_output" + $ext
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60 #set untrimmed_output = "untrimmed_output" + $ext
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61 ln -f -s '${input_1}' '$read1' &&
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62
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63 #if $paired:
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64 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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65 #set ext2 = ".fq.gz"
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66 #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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67 #set ext2 = ".fq.gz"
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68 #else if $input_2.is_of_type('fasta'):
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69 #set ext2 = ".fa"
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70 #else:
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71 #set ext2 = ".fq"
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72 #end if
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73 #set read2 = $read2 + $ext2
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74 #set out2 = "out2" + $ext2
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75 #set too_short_paired_output = "too_short_paired_output" + $ext2
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76 #set too_long_paired_output = "too_long_paired_output" + $ext2
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77 #set untrimmed_paired_output = "untrimmed_paired_output" + $ext2
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78 ln -f -s '${input_2}' '$read2' &&
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79 #end if
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80
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81 ## Run Cutadapt
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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82
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83 #if 'multiple_output' in $output_selector:
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84 mkdir split &&
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85 #end if
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86
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87 cutadapt
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88
24
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iuc
parents: 23
diff changeset
89 -j=\${GALAXY_SLOTS:-4}
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
90
27
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iuc
parents: 26
diff changeset
91 #if 'json_stats' in $output_selector:
35
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iuc
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diff changeset
92 --json stats.json
27
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iuc
parents: 26
diff changeset
93 #end if
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
94
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
95 #if str( $library.type ) == "single":
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
96 @read1_options@
24
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iuc
parents: 23
diff changeset
97 #if 'multiple_output' in $output_selector:
18
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iuc
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diff changeset
98 --output='split/{name}.${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
99 #else:
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
100 --output='$out1'
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
101 #end if
13
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iuc
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diff changeset
102 #else:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
103 @read1_options@
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
104 @read2_options@
29
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iuc
parents: 28
diff changeset
105 --output='$out1'
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
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diff changeset
106 --paired-output='$out2'
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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107 #end if
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
108
13
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iuc
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109 --error-rate=$adapter_options.error_rate
24
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iuc
parents: 23
diff changeset
110 --times=$adapter_options.times
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
111 --overlap=$adapter_options.overlap
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
112 $adapter_options.no_indels
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
113 $adapter_options.match_read_wildcards
35
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iuc
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diff changeset
114 $adapter_options.no_match_adapter_wildcards
24
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iuc
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diff changeset
115 --action=$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
116 $adapter_options.revcomp
11
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iuc
parents: 10
diff changeset
117
24
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iuc
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diff changeset
118 $filter_options.discard_trimmed
13
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iuc
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diff changeset
119 $filter_options.discard_untrimmed
24
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iuc
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diff changeset
120
35
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iuc
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diff changeset
121 #if str($filter_options.minimum_length) and str($library.type) != "single" and str($library.minimum_length2) != '':
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
122 --minimum-length=$filter_options.minimum_length:$library.minimum_length2
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
123 #else if str($filter_options.minimum_length):
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
124 --minimum-length=$filter_options.minimum_length
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
125 #end if
35
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iuc
parents: 33
diff changeset
126 #if str($filter_options.maximum_length) and str($library.type) != "single" and str($library.maximum_length2) != '':
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
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diff changeset
127 --maximum-length=$filter_options.maximum_length:$library.maximum_length2
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
128 #else if str($filter_options.maximum_length):
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
129 --maximum-length=$filter_options.maximum_length
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
130 #end if
22
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iuc
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diff changeset
131 #if str($filter_options.max_n):
13
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iuc
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132 --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
133 #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
134 #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
135 #if $filter_options.pair_filter:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
136 --pair-filter=$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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diff changeset
137 #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
138 #end if
24
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iuc
parents: 23
diff changeset
139 #if str($filter_options.max_expected_errors):
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
140 --max-expected-errors=$filter_options.max_expected_errors
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
141 #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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diff changeset
142 $filter_options.discard_cassava
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
143
35
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iuc
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diff changeset
144 #if $input_1.ext.startswith("fastqillumina") or $input_1.ext.startswith("fastqsolexa")
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
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diff changeset
145 --quality-base=64
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iuc
parents: 33
diff changeset
146 #end if
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
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diff changeset
147
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
148 #if str($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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diff changeset
149 --quality-cutoff=$read_mod_options.quality_cutoff
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
150 #end if
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
151 #if str($read_mod_options.nextseq_trim) != '0':
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
152 --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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diff changeset
153 #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
154 $read_mod_options.trim_n
35
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iuc
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diff changeset
155 $read_mod_options.poly_a
28
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iuc
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diff changeset
156 #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
157 --strip-suffix $read_mod_options.strip_suffix
c053d4cad713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 9ec830a98da45d5fb2f92a817c7cd0376504be90"
iuc
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diff changeset
158 #end if
24
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iuc
parents: 23
diff changeset
159 #if str($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
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diff changeset
160 #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
161 --length=$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
162 #else
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
163 --length=-$read_mod_options.shorten_options.length
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
164 #end if
13
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iuc
parents: 12
diff changeset
165 #end if
24
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iuc
parents: 23
diff changeset
166 #if str($read_mod_options.length_tag) != '':
22
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iuc
parents: 21
diff changeset
167 --length-tag='$read_mod_options.length_tag'
13
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
168 #end if
24
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iuc
parents: 23
diff changeset
169 #if str($read_mod_options.rename) != '':
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
170 --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
diff changeset
171 #end if
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
172 $read_mod_options.zero_cap
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
173
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
174
13
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iuc
parents: 12
diff changeset
175 '${read1}'
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
parents: 12
diff changeset
176 #if $paired:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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diff changeset
177 '${read2}'
27
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iuc
parents: 26
diff changeset
178 #if $library.r2.quality_cutoff2:
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
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179 -Q=$library.r2.quality_cutoff2
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180 #end if
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181 #end if
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182
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183 #if 'report' in $output_selector:
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184 > report.txt
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185 #end if
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186 ]]></command>
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187 <inputs>
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188
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189 <!-- Reads -->
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190 <conditional name="library">
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191 <param name="type" type="select" label="Single-end or Paired-end reads?">
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192 <option value="single">Single-end</option>
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193 <option value="paired">Paired-end</option>
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194 <option value="paired_collection">Paired-end Collection</option>
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195 </param>
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196
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197 <when value="single">
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198 <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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199 <expand macro="single_end_options" />
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200 </when>
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201
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202 <when value="paired">
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203 <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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204 <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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205 <expand macro="paired_end_options" />
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206 </when>
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207
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208 <when value="paired_collection">
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209 <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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210 <expand macro="paired_end_options" />
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211 </when>
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212
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213 </conditional>
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214
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215 <!-- Adapter Options -->
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216 <section name="adapter_options" title="Adapter Options">
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217 <param name="action" type="select" label="What to do if a match is found">
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218 <option value="trim" selected="true">Trim: trim adapter and upstream or downstream sequence</option>
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219 <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
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220 <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
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221 <option value="lowercase">Lowercase: convert to lowercase</option>
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222 <option value="none">None: leave unchanged</option>
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223 </param>
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224 <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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225 <param argument="--no-indels" type="boolean" checked="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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226 <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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227 <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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228 <param argument="--match-read-wildcards" type="boolean" checked="false" truevalue="--match-read-wildcards" falsevalue="" label="Match wilcards in reads" help="Interpret IUPAC wildcards in reads"/>
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229 <param argument="--no-match-adapter-wildcards" type="boolean" checked="true" truevalue="" falsevalue="--no-match-adapter-wildcards" label="Match wilcards in adapters" help="Interpret IUPAC wildcards in adapters."/>
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230 <param argument="--revcomp" type="boolean" checked="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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231 </section>
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232
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233 <!-- Filter Options -->
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234 <section name="filter_options" title="Filter Options">
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235 <param argument="--discard-trimmed" type="boolean" checked="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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236 <param argument="--discard_untrimmed" type="boolean" checked="false" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
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237 <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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238 <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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239 <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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240 <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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241 <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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242 <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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243 <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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244
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245 </param>
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246 <param argument="--max-expected-errors" type="float" 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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247 <param argument="--max-average-error-rate" type="float" min="0" max="1" optional="true" value="" label="Max average expected errors" help="As --max-expected-errors (see above), but divided by length to account for reads of varying length" />
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248 <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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249 </section>
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250
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251 <!-- Read Modification Options -->
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252 <section name="read_mod_options" title="Read Modification Options">
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253 <param argument="--cut" type="integer" value="0" optional="true" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." />
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254 <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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255 <sanitizer>
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256 <valid initial="string.digits"><add value="," /></valid>
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257 </sanitizer>
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258 <validator type="regex">[0-9]+(,[0-9])?</validator>
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259 </param>
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260 <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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261 <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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262 <param argument="--poly-a" type="boolean" truevalue="--poly-a" falsevalue="" checked="false" label="Trim poly-A tails" help="Note, this trim poly-T 'heads' on R2"/>
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263 <param argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
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264 <conditional name="shorten_options">
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265 <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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266 <option value="True">Enabled</option>
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267 <option value="False" selected="true">Disabled</option>
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268 </param>
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269 <when value="True">
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270 <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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271 <param name="shorten_end" type="select" label="End at which to apply the slice">
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272 <option value="3prime">3' ends</option>
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273 <option value="5prime">5' ends</option>
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274 </param>
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275 </when>
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276 <when value="False">
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277 </when>
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278 </conditional>
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279 <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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280 <sanitizer invalid_char="">
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281 <valid initial="string.letters,string.digits">
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282 <add value="/" />
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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 </valid>
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289 </sanitizer>
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290 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
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291 </param>
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292 <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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293 <sanitizer invalid_char="">
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294 <valid initial="string.letters,string.digits">
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295 <add value="{" />
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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 </valid>
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301 </sanitizer>
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302 <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
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303 </param>
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304 <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="false" label="Change negative quality values to zero" />
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305 </section>
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306
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307 <!-- Output Options -->
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308 <param name="output_selector" type="select" multiple="true" display="checkboxes" label="Outputs selector">
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309 <option value="report">Report: Cutadapt's per-adapter statistics. You can use this file with MultiQC.</option>
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310 <option value="info_file">Info file: write information about each read and its adapter matches.</option>
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311 <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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312 <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
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313 <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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314 <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
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315 <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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316 <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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317 <option value="json_stats">Statistics in JSON format</option>
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318 </param>
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319 </inputs>
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320
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321 <outputs>
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322 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output">
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323 <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter>
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324 <expand macro="inherit_format_1" />
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325 </data>
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326
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327 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" >
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328 <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter>
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329 <expand macro="inherit_format_2" />
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330 </data>
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331
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332 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
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333 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
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334 <data name="forward" from_work_dir="out1.*" />
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335 <data name="reverse" from_work_dir="out2.*" />
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336 </collection>
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337
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338 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
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339 <filter>output_selector and 'report' in output_selector</filter>
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340 </data>
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341 <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
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342 <filter>output_selector and 'info_file' in output_selector</filter>
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343 </data>
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344
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345 <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
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346 <filter>output_selector and 'rest_file' in output_selector</filter>
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347 <expand macro="inherit_format_1" />
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lparsons
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348 </data>
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349
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350 <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
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351 <filter>output_selector and 'wildcard_file' in output_selector</filter>
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lparsons
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352 </data>
11
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353
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354 <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
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355 <filter>output_selector and 'untrimmed_file' in output_selector</filter>
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356 <expand macro="inherit_format_1" />
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lparsons
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357 </data>
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358 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
24
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iuc
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359 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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360 <filter>output_selector and 'untrimmed_file' in output_selector </filter>
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361 <expand macro="inherit_format_2" />
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362 </data>
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363
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iuc
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diff changeset
364 <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
24
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iuc
parents: 23
diff changeset
365 <filter>output_selector and 'too_short_file' in output_selector</filter>
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iuc
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366 <expand macro="inherit_format_1" />
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lparsons
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367 </data>
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diff changeset
368 <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
24
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369 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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370 <filter>output_selector and 'too_short_file' in output_selector</filter>
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371 <expand macro="inherit_format_2" />
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lparsons
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372 </data>
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diff changeset
373 <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
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diff changeset
374 <filter>output_selector and 'too_long_file' in output_selector</filter>
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parents: 11
diff changeset
375 <expand macro="inherit_format_1" />
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iuc
parents: 10
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376 </data>
20
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iuc
parents: 19
diff changeset
377 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
24
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iuc
parents: 23
diff changeset
378 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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parents: 23
diff changeset
379 <filter>output_selector and 'too_long_file' in output_selector</filter>
12
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iuc
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380 <expand macro="inherit_format_2" />
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lparsons
parents: 8
diff changeset
381 </data>
27
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iuc
parents: 26
diff changeset
382 <data name="json_stats" format="json" from_work_dir="stats.json" label="${tool.name} on ${on_string}: Statistics (JSON)" >
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
383 <filter>output_selector and 'json_stats' in output_selector</filter>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
384 </data>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
385 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" format="fastqsanger" >
18
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iuc
parents: 17
diff changeset
386 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
24
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iuc
parents: 23
diff changeset
387 <filter>output_selector and 'multiple_output' in output_selector</filter>
16
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iuc
parents: 15
diff changeset
388 </collection>
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lparsons
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diff changeset
389 </outputs>
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lparsons
parents: 8
diff changeset
390
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lparsons
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diff changeset
391 <tests>
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diff changeset
392 <!-- Ensure fastq works -->
23
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iuc
parents: 22
diff changeset
393 <test expect_num_outputs="1">
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diff changeset
394 <param name="type" value="single" />
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iuc
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diff changeset
395 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
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iuc
parents: 24
diff changeset
396 <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
397 <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
398 <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
399 <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
400 <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
401 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
402 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
403 </section>
12
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iuc
parents: 11
diff changeset
404 <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
11
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iuc
parents: 10
diff changeset
405 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
406 <!-- 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
407 <test expect_num_outputs="1">
11
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iuc
parents: 10
diff changeset
408 <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
409 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
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iuc
parents: 24
diff changeset
410 <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
411 <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
412 <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
413 <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
414 <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
415 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
416 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
417 </section>
35
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diff changeset
418 <output name="out1" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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diff changeset
419 </test>
11
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iuc
parents: 10
diff changeset
420 <!-- Ensure paired 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
421 <test expect_num_outputs="2">
11
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iuc
parents: 10
diff changeset
422 <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
423 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
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iuc
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diff changeset
424 <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
425 <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
426 <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
427 <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
428 <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
429 <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
430 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
431 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
432 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
433 <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
434 <repeat name="adapters2">
35
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iuc
parents: 33
diff changeset
435 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
436 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
437 <param name="adapter" value="AGATCGGAAGAGC"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
438 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
439 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
440 </section>
35
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iuc
parents: 33
diff changeset
441 <output name="out1" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
442 <output name="out2" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
21
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iuc
parents: 20
diff changeset
443 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
444 <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
445 <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
446 <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
447 <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
448 <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
449 <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
450 </assert_command>
12
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iuc
parents: 11
diff changeset
451 </test>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
452 <!-- 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
453 <test expect_num_outputs="3">
12
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iuc
parents: 11
diff changeset
454 <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
455 <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
456 <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
457 <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
458 <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
459 </collection>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
460 </param>
25
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iuc
parents: 24
diff changeset
461 <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
462 <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
463 <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
464 <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
465 <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
466 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
467 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
468 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
469 <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
470 <repeat name="adapters2">
35
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iuc
parents: 33
diff changeset
471 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
472 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
473 <param name="adapter" value="AGATCGGAAGAGC"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
474 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
475 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
476 </section>
29
48f587c13075 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
iuc
parents: 28
diff changeset
477 <output_collection name="out_pairs" type="paired" count="2">
35
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iuc
parents: 33
diff changeset
478 <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
479 <element name="reverse" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
480 </output_collection>
11
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iuc
parents: 10
diff changeset
481 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
482 <!-- 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
483 <test expect_num_outputs="1">
11
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iuc
parents: 10
diff changeset
484 <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
485 <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
486 <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
487 <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
488 <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
489 <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
490 <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
491 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
492 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
493 </section>
12
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iuc
parents: 11
diff changeset
494 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
11
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iuc
parents: 10
diff changeset
495 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
496 <!-- 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
497 <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
498 <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
499 <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
500 <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
501 <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
502 <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
503 <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
504 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
505 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
506 </section>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
507 <section name="filter_options">
35
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iuc
parents: 33
diff changeset
508 <param name="discard_trimmed" value="true"/>
21
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iuc
parents: 20
diff changeset
509 </section>
12
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iuc
parents: 11
diff changeset
510 <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
511 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
512 <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
513 </assert_command>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
514 </test>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
515 <!-- 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
516 <test expect_num_outputs="3">
11
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iuc
parents: 10
diff changeset
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
523 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
524 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
525 </section>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
526 <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
527 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
528 <!--allow for differing schema, cutadapt and python version as well as two lines containing the number of cores -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
529 <output name="json_stats" file="cutadapt_rest.json" ftype="json" lines_diff="10"/>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
530 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
531 </test>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
532 <!-- 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
533 <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
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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
541 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
542 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
543 </section>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
544 <param name="nextseq_trim" value="20" />
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
545 <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
546 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
547 <!-- 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
548 <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
549 <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
550 <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
551 <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
552 <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
553 <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
554 <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
555 <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
556 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
557 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
558 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
559 <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
560 <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
561 <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
562 <assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
563 <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
564 </assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
565 </output>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
566 <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
567 </test>
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
568
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
569
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
570 <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
571 <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
572 <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
573 <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
574 <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
575 <repeat name="front_adapters">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
576 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
577 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
578 <param name="adapter_name" value="A1" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
579 <param name="adapter" value="^GTCGGTAA" />
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
580 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
581 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
582 <repeat name="front_adapters">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
583 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
584 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
585 <param name="adapter_name" value="A2" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
586 <param name="adapter" value="^AGGTCACT" />
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
587 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
588 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
589 </section>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
590 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
591 <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
592 <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
593 <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
594 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
595 <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
596 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
597 <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
598 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
599 </output_collection>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
600 </test>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
601
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
602 <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
603 <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
604 <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
605 <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
606 <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
607 <repeat name="front_adapters">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
608 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
609 <param name="adapter_source_list" value="file"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
610 <param name="adapter_file" ftype="fasta" value="barcodes.fasta" />
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>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
612 </repeat>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
613 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
614 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
615 <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
616 <output_collection name="split_output" type="list" count="3">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
617 <element name="A1" decompress="true" file="A1.fastq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
618 <element name="A2" decompress="true" file="A2.fastq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
619 <element name="unknown" decompress="true" file="unknown.fastq.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
620 </output_collection>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
621 </test>
18
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
622
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
623 <!-- 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
624 <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
625 <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
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
633 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
634 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
635 <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
636 <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
637 <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
638 </test>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
639 <!-- 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
640 <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
641 <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
642 <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
643 <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
644 <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
645 <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
646 <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
647 <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
648 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
649 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
650 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
651 <param name="output_selector" value="untrimmed_file" />
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
652 <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
653 <!--
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
654 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
655 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
656 `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
657 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
658 -->
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
659 <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
660 </test>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
661 <!-- 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
662 <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
663 <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
664 <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
665 <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
666 <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
667 <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
668 <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
669 <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
670 <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
671 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
672 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
673 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
674 <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
675 <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
676 <conditional name="adapter_source">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
677 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
678 <param name="adapter" value="AGATCGGAAGAGC"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
679 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
680 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
681 </section>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
682 <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
683 <param name="discard_untrimmed" value="true"/>
24
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iuc
parents: 23
diff changeset
684 <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
685 <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
686 <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
687 <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
688 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
689 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
690 <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
691 <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
692 <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
693 <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
694 </assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
695 </test>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
696 <!-- 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
697 <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
698 <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
699 <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
700 <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
701 <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
702 <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
703 <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
704 <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
705 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
706 </repeat>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
707 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
708 <param name="cut" value="5"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
709 <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
710 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
711 <!-- 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
712 <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
713 <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
714 <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
715 <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
716 <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
717 <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
718 <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
719 <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
720 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
721 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
722 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
723 <param name="cut" value="5"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
724 <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
725 <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
726 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
727 <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
728 <assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
729 <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
730 </assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
731 </output>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
732 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
733 <!-- 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
734 <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
735 <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
736 <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
737 <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
738 <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
739 <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
740 <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
741 <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
742 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
743 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
744 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
745 <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
746 <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
747 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
748 <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
749 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
750 <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
751 <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
752 <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
753 <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
754 <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
755 <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
756 <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
757 <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
758 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
759 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
760 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
761 <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
762 <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
763 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
764 <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
765 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
766 <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
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 <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
774 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
775 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
776 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
777 <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
778 <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
779 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
780 <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
781 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
782 <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
783 <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
784 <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
785 <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
786 <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
787 <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
788 <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
789 <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
790 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
791 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
792 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
793 <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
794 <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
795 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
796 <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
797 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
798 <!-- 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
799 <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
800 <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
801 <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
802 <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
803 <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
804 <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
805 <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
806 <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
807 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
808 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
809 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
810 <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
811 <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
812 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
813 <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
814 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
815 <!-- 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
816 <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
817 <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
818 <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
819 <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
820 <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
821 <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
822 <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
823 <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
824 <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
825 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
826 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
827 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
828 <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
829 <repeat name="adapters2">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
830 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
831 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
832 <param name="adapter" value="CTACAAG"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
833 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
834 </repeat>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
835 <param name="minimum_length2" value="10"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
836 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
837 <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
838 <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
839 <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
840 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
841 <output name="out1" decompress="true" file="cutadapt_out1_min_length.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
842 <output name="out2" decompress="true" file="cutadapt_out2_min_length.fq.gz" ftype="fastq.gz"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
843 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
844 <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
845 <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
846 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
847 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
848 <!-- 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
849 <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
850 <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
851 <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
852 <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
853 <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
854 <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
855 <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
856 <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
857 <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
858 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
859 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
860 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
861 <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
862 <repeat name="adapters2">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
863 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
864 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
865 <param name="adapter" value="AGATCGGAAGAGC"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
866 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
867 </repeat>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
868 <param name="maximum_length2" value="30"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
869 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
870 <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
871 <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
872 <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
873 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
874 <output name="out1" decompress="true" file="cutadapt_out1_max_length.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
875 <output name="out2" decompress="true" file="cutadapt_out2_max_length.fq.gz" ftype="fastq.gz"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
876 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
877 <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
878 <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
879 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
880 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
881 <!-- 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
882 <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
883 <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
884 <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
885 <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
886 <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
887 <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
888 <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
889 <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
890 <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
891 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
892 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
893 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
894 <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
895 <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
896 <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
897 <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
898 <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
899 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
900 </repeat>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
901 <param name="maximum_length2" value="30"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
902 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
903 <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
904 <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
905 <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
906 <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
907 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
908 <output name="out1" decompress="true" file="cutadapt_out1_max_min_01.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
909 <output name="out2" decompress="true" file="cutadapt_out2_max_min_01.fq.gz" ftype="fastq.gz"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
910 <assert_command>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
911 <has_text text="--minimum-length=10"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
912 <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
913 <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
914 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
915 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
916 <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
917 <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
918 <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
919 <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
920 <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
921 <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
922 <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
923 <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
924 <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
925 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
926 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
927 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
928 <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
929 <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
930 <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
931 <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
932 <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
933 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
934 </repeat>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
935 <param name="minimum_length2" value="10"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
936 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
937 <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
938 <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
939 <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
940 <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
941 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
942 <output name="out1" decompress="true" file="cutadapt_out1_max_min_02.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
943 <output name="out2" decompress="true" file="cutadapt_out2_max_min_02.fq.gz" ftype="fastq.gz"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
944 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
945 <has_text text="--minimum-length=10:10"/>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
946 <has_text text="--maximum-length=50"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
947 <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
948 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
949 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
950 <!-- 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
951 <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
952 <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
953 <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
954 <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
955 <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
956 <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
957 <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
958 <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
959 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
960 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
961 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
962 <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
963 <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
964 <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
965 <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
966 <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
967 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
968 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
969 <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
970 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
971 <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
972 <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
973 <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
974 <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
975 <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
976 <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
977 <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
978 <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
979 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
980 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
981 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
982 <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
983 <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
984 <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
985 <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
986 <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
987 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
988 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
989 <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
990 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
991 <!-- 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
992 <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
993 <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
994 <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
995 <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
996 <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
997 <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
998 <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
999 <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
1000 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1001 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1002 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1003 <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
1004 <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
1005 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1006 <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
1007 </test>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1008
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1009 <!-- 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
1010 <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
1011 <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
1012 <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
1013 <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
1014 <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
1015 <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
1016 <param name="adapter_source_list" value="user"/>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1017 <param name="adapter" value="GAANTAGCTACCACX"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1018 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1019 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1020 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1021 <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
1022 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1023 <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
1024 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1025 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1026 <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
1027 <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
1028 <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
1029 <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
1030 <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
1031 <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
1032 <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
1033 <param name="adapter_source_list" value="user"/>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1034 <param name="adapter" value="AGATCGGAAGAGCX"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1035 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1036 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1037 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1038 <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
1039 <repeat name="adapters2">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1040 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1041 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1042 <param name="adapter" value="AGATCGGAAGAGCX"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1043 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1044 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1045 </section>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1046 <output name="out1" decompress="true" file="cutadapt_out1_internal_adapter.fq.gz" ftype="fastq.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1047 <output name="out2" decompress="true" file="cutadapt_out2_internal_adapter.fq.gz" ftype="fastq.gz"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1048 <assert_command>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1049 <has_text text="'AGATCGGAAGAGCX'" n="2"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1050 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1051 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1052 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1053 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1054 <param name="input_1" ftype="fastq" 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
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="builtin"/>
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="TGTAGGCC"/>
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>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1063 <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
1064 <assert_command>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1065 <has_text text="'TGTAGGCC'"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1066 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1067 </test>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1068 <!-- 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
1069 <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
1070 <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
1071 <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
1072 <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
1073 <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
1074 <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
1075 </collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1076 </param>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1077 <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
1078 <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
1079 <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
1080 <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
1081 <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
1082 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1083 <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
1084 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1085 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1086 <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
1087 <repeat name="adapters2">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1088 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1089 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1090 <param name="adapter" value="AGATCGGAAGAGC"/>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1091 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1092 <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
1093 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1094 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1095 <output_collection name="out_pairs" type="paired">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1096 <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1097 <element name="reverse" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1098 </output_collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1099 </test>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1100 <!-- 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
1101 <test expect_num_outputs="3">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1102 <param name="type" value="paired_collection" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1103 <param name="input_1">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1104 <collection type="paired">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1105 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1106 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1107 </collection>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1108 </param>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1109 <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
1110 <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
1111 <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
1112 <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
1113 <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
1114 <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
1115 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1116 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1117 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1118 <section name="r2">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1119 <repeat name="adapters2">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1120 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1121 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1122 <param name="adapter" value="AGATCGGAAGAGC"/>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1123 </conditional>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1124 </repeat>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1125 <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
1126 </section>
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1127 <output_collection name="out_pairs" type="paired">
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1128 <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1129 <element name="reverse" decompress="true" file="cutadapt_out2_cutoff.fq.gz" ftype="fastq.gz" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1130 </output_collection>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1131 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1132 <has_text text="--quality-cutoff=5"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1133 <has_text text="-Q=15,20"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1134 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1135 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1136
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1137 <!-- ployA trimmining https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_paired.py#L768 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1138 <test expect_num_outputs="3">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1139 <param name="type" value="paired_collection" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1140 <param name="input_1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1141 <collection type="paired">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1142 <element name="forward" ftype="fasta" value="cutadapt/data/polya.1.fasta" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1143 <element name="reverse" ftype="fasta" value="cutadapt/data/polya.2.fasta" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1144 </collection>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1145 </param>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1146 <param name="poly_a" value="true"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1147 <output_collection name="out_pairs" type="paired">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1148 <element name="forward" file="cutadapt/cut/polya.1.fasta" ftype="fasta" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1149 <element name="reverse" file="cutadapt/cut/polya.2.fasta" ftype="fasta" />
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
iuc
parents: 26
diff changeset
1150 </output_collection>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1151 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1152 <has_text text="--poly-a"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1153 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1154 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1155
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1156 <!-- polyA legacy https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L267 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1157 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1158 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1159 <param name="input_1" ftype="fasta" value="cutadapt/data/polya.1.fasta" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1160 <section name="r1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1161 <repeat name="adapters">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1162 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1163 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1164 <param name="adapter" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1165 </conditional>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1166 </repeat>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1167 </section>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1168 <param name="overlap" value="10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1169 <output name="out1" file="cutadapt/cut/polya.legacy.1.fasta" ftype="fasta"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1170 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1171 <has_text text="-a 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1172 <has_text text="--overlap=10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1173 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1174 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1175
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1176 <!-- polyA legacy brace notation https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L276 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1177 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1178 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1179 <param name="input_1" ftype="fasta" value="cutadapt/data/polya.1.fasta" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1180 <section name="r1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1181 <repeat name="adapters">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1182 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1183 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1184 <param name="adapter" value="A{35}"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1185 </conditional>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1186 </repeat>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1187 </section>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1188 <param name="overlap" value="10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1189 <output name="out1" file="cutadapt/cut/polya.legacy.1.fasta" ftype="fasta"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1190 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1191 <has_text text="-a 'A{35}'"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1192 <has_text text="--overlap=10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1193 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1194 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1195
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1196 <!-- polyA https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L281 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1197 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1198 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1199 <param name="input_1" ftype="fasta" value="cutadapt/data/polya.1.fasta" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1200 <param name="poly_a" value="true"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1201 <output name="out1" file="cutadapt/cut/polya.1.fasta" ftype="fasta"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1202 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1203 <has_text text="--poly-a"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1204 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1205 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1206
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1207 <!-- fasta.gz input https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L78
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1208 in contrast to the original test the tool automatically compresses the output -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1209 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1210 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1211 <param name="input_1" ftype="fasta.gz" value="cutadapt/data/simple.fasta.gz" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1212 <output name="out1" decompress="true" file="cutadapt/cut/simple.fasta.gz" ftype="fasta.gz"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1213 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1214
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1215 <!-- fatstqillumina input https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L252 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1216 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1217 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1218 <param name="input_1" ftype="fastqillumina" value="cutadapt/data/illumina64.fastq" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1219 <section name="r1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1220 <repeat name="adapters">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1221 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1222 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1223 <param name="adapter" value="XXXXXX"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1224 </conditional>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1225 </repeat>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1226 </section>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1227 <param name="quality_cutoff" value="10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1228 <output name="out1" file="cutadapt/cut/illumina64.fastq" ftype="fastqillumina"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1229 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1230 <has_text text="-a 'XXXXXX'"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1231 <has_text text="--quality-cutoff=10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1232 <has_text text="--quality-base=64"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1233 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1234 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1235 <!-- fatstqillumina input https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L257 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1236 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1237 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1238 <param name="input_1" ftype="fastqillumina" value="cutadapt/data/illumina64.fastq" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1239 <param name="quality_cutoff" value="10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1240 <output name="out1" file="cutadapt/cut/illumina64.fastq" ftype="fastqillumina"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1241 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1242 <has_text text="--quality-cutoff=10"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1243 <has_text text="--quality-base=64"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1244 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1245 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1246
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1247 <!-- https://github.com/marcelm/cutadapt/blame/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L1028 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1248 <test expect_num_outputs="3">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1249 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1250 <param name="input_1" ftype="fastqillumina" value="cutadapt/data/maxee.fastq" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1251 <param name="max_expected_errors" value="0.9"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1252 <param name="output_selector" value="report,info_file"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1253 <output name="out1" file="cutadapt/cut/maxee.fastq" ftype="fastqillumina"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1254 <output name="report">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1255 <assert_contents>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1256 <has_text text="Reads with too many exp. errors: 2"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1257 </assert_contents>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1258 </output>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1259 <output name="info_file">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1260 <assert_contents>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1261 <has_n_lines n="4"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1262 <has_text text="ee_0.8&#09;-1&#09;ACGTTGCA&#09;++++++++"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1263 </assert_contents>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1264 </output>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1265 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1266 <has_text text="--max-expected-errors=0.9"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1267 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1268 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1269
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1270 <!-- https://github.com/marcelm/cutadapt/blob/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L335 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1271 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1272 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1273 <param name="input_1" ftype="fasta" value="cutadapt/data/wildcard.fa" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1274 <section name="r1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1275 <repeat name="anywhere_adapters">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1276 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1277 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1278 <param name="adapter" value="ACGTACGT"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1279 </conditional>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1280 </repeat>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1281 </section>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1282 <section name="adapter_options">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1283 <param name="match_read_wildcards" value="true"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1284 </section>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1285 <output name="out1" file="cutadapt/cut/wildcard.fa" ftype="fasta" sort="true"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1286 <assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1287 <has_text text="--match-read-wildcards"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1288 <has_text text="-b 'ACGTACGT'"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1289 </assert_command>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1290 </test>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1291
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1292 <!-- https://github.com/marcelm/cutadapt/blob/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L368 -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1293 <test expect_num_outputs="1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1294 <param name="type" value="single" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1295 <param name="input_1" ftype="fasta" value="cutadapt/data/wildcardN.fa" />
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1296 <section name="r1">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1297 <repeat name="adapters">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1298 <conditional name="adapter_source">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1299 <param name="adapter_source_list" value="user"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1300 <param name="adapter" value="GGGGGGG"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1301 </conditional>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1302 </repeat>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 33
diff changeset
1303 </section>
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1304 <section name="adapter_options">
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1305 <param name="match_read_wildcards" value="true"/>
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1306 <param name="error_rate" value="0"/>
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1307 </section>
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diff changeset
1308 <output name="out1" file="cutadapt/cut/wildcardN.fa" ftype="fasta" sort="true"/>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
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1309 <assert_command>
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1310 <has_text text="--match-read-wildcards"/>
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1311 <has_text text="--error-rate=0.0"/>
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diff changeset
1312 <has_text text="-a 'GGGGGGG'"/>
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1313 </assert_command>
27
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
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1314 </test>
9
93d58ffe39f1 Updated to version 1.6
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1315 </tests>
0
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1316
11
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1317 <help><![CDATA[
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1318
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1319 .. class:: infomark
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1320
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1321 **What it does**
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1322
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1323 -------------------
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1324
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1325 **Cutadapt** finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
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1326
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1327 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.
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1328
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1329 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.
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1330
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1331 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.
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1332
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1333 -------------------
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1334
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diff changeset
1335 **Inputs**
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1336
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1337 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1338
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1339 Input files for Cutadapt need to be:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1340
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diff changeset
1341 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
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1342
19
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1343 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
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Lance Parsons <lparsons@princeton.edu>
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1344
11
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1345 ============================================= ===================
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1346 **Option** **Sequence**
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1347 --------------------------------------------- -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1348 3’ (End) Adapter ADAPTER
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1349 Anchored 3’ Adapter ADAPTER$
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Lance Parsons <lparsons@princeton.edu>
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diff changeset
1350
11
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1351 5’ (Front) Adapter ADAPTER
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1352 Anchored 5’ Adapter ^ADAPTER
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1353
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1354 5’ or 3’ (Both possible) ADAPTER
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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diff changeset
1355
11
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1356 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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1357 Non-anchored Linked Adapter - 5' (Front) only ADAPTER1...ADAPTER2
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1358 ============================================= ===================
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diff changeset
1359
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1360 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
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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 .. image:: $PATH_TO_IMAGES/adapters.svg
0
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Lance Parsons <lparsons@princeton.edu>
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diff changeset
1363
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diff changeset
1364
11
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1365 -------------------
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1366
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1367 *Example: Illumina TruSeq Adapters*
0
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1368
11
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1369 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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diff changeset
1370
11
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1371 If you have reads containing Illumina TruSeq adapters, for example, follow these steps.
0
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1372
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1373
11
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1374 For Single-end reads as well as the first reads of Paired-end data:
0
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1375
11
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1376 **Read 1**
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1377
11
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1378 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
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1379
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1380 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
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1381
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1382
11
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1383 For the second reads of Paired-end data:
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1384
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1385 **Read 2**
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1386
11
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1387 In the **3' (End) Adapters** option above, insert the reverse complement of the “TruSeq Universal Adapter”:
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1388
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1389 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
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1390
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1391 The adapter sequences can be found in the document `Illumina TruSeq Adapters De-Mystified`_.
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1392
11
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1393 -----------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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1394
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1395 **Outputs**
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1396
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1397 -----------
0
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parents:
diff changeset
1398
11
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1399 - Trimmed reads
8
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lparsons
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1400
11
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diff changeset
1401 Optionally, under **Output Options** you can choose to output
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1402
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1403 * Report
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iuc
parents: 10
diff changeset
1404 * Info file
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1405
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1406
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1407 **Report**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1408
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1409 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
1410
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1411 Example:
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1412
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1413 ::
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1414
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1415 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
1416
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1417 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
1418 --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
1419
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1420 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
1421 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
1422
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1423 === Summary ===
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1424
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1425 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
1426 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
1427 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
1428 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
1429 Pairs written (passing filters): 96 (97.0%)
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1430
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1431 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
1432 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
1433 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
1434 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
1435 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
1436 Read 2: 24,081 bp
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1437
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1438
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1439 **Info file**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1440
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1441 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
1442
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1443 Columns contain the following data:
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1444
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1445 * **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
1446 * **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
1447 * **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
1448 * **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
1449 * **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
1450 * **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
1451 * **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
1452 * **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
1453 * **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
1454 * **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
1455 * **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
1456
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1457 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
1458
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1459 If no adapter was found, the format is as follows:
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1460
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1461 #. Read name
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1462 #. 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
1463 #. 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
1464 #. Quality values
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1465
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1466 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
1467
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1468 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
1469
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1470
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1471 --------------------
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1472
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1473 **Rename Reads**
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1474
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1475 --------------------
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1476
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1477
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1478 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
1479
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1480 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.
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1481
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1482 The following placeholders are currently available for single-end reads:
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1483
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1484 * {header} – the full, unchanged header
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1485 * {id} – the read ID, that is, the part of the header before the first whitespace
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1486 * {comment} – the part of the header after the whitespace following the ID
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1487 * {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.
30
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
iuc
parents: 29
diff changeset
1488 * {match_sequence} – the sequence of the read that matched the adapter (including errors). If there was no adapter match, this is set to an empty string. If you use a linked adapter, this is to the two matching strings, separated by a comma.
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1489 * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1490 * {cut_suffix} – the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument)
30
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
iuc
parents: 29
diff changeset
1491 * {rc} – this is replaced with the string rc if the read was reverse complemented. This only applies when reverse complementing was requested
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1492
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1493 If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1’s comment in R1 and it becomes R2’s comment in R2.
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1494
30
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
iuc
parents: 29
diff changeset
1495 For paired-end data, the placeholder {rn} is available (“read number”), and it is replaced with 1 in R1 and with 2 in R2.
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
iuc
parents: 29
diff changeset
1496
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1497 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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1498 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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1499
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1500 --------------------
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1501
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1502 **More Information**
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1503
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1504 --------------------
9
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1505
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1506 See the excellent `Cutadapt documentation`_
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1507
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1508 .. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/
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1509 .. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html
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1510 .. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf
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1511
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1512
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1513 --------------------
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1514
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1515 **Galaxy Wrapper Development**
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1516
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1517 --------------------
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1518
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1519 Author: Lance Parsons <lparsons@princeton.edu>
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1520
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1521 ]]></help>
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1522 <expand macro="citations" />
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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1523 </tool>