Mercurial > repos > iuc > presto_maskprimers

annotate presto_maskprimers.xml @ 4:df0797c61790 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
author iuc
date Fri, 04 Oct 2024 09:04:50 +0000
parents 98b0b4c22e69
children
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98b0b4c22e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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1 <tool id="presto_maskprimers" name="pRESTO MaskPrimers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Removes primers and annotates sequences with primer and barcode identifiers.</description>
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3 <macros>
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4 <import>presto_macros.xml</import>
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5 </macros>
4
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6 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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10 <version_command>MaskPrimers.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
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13 ln -s '$primers_in' primers.fasta &&
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14 MaskPrimers.py '$cc.command'
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15 --nproc "\${GALAXY_SLOTS:-1}"
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16 -s in.fastq
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17 -p primers.fasta
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18 --mode '$mode'
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19 --maxerror '$maxerror'
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20 $revpr
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21 $barcode
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23 #if $cc.command == "align"
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24 --maxlen '$cc.maxlen'
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25 --gap '$cc.gap_open' '$cc.gap_extend'
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26 $cc.skiprc
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27 #end if
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29 #if $cc.command == "score"
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30 --start '$cc.start'
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31 #end if
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32
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33 --outdir=.
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34 --outname=tmp_mask
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35 #if $capture_log
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36 --log '$log_out'
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
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41 <param argument="-p" name="primers_in" type="data" format="fasta" label="Primer FASTA file"/>
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42 <param argument="--mode" type="select" value="mask" label="Mode" help="Specifies how identified primer sequences will be handled.">
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43 <option value="cut">Remove primer and preceding sequence (cut)</option>
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44 <option value="mask">Mask primer to Ns and remove preceding sequence (mask)</option>
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45 <option value="trim">Leave primer intact and remove preceding sequence (trim)</option>
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46 <option value="tag">Leave primer and preceding sequence intact (tag)</option>
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47 </param>
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48 <conditional name="cc">
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49 <param name="command" type="select" label="Command">
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50 <option value="align">Find primer matches using pairwise local alignment (align)</option>
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51 <option value="score">Find primer matches by scoring primers at a fixed position (score)</option>
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52 </param>
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53 <when value="align">
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54 <param argument="--maxlen" type="integer" value="50" label="Max Length" help="Maximum length of sequence window to search for primers."/>
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55 <param argument="--skiprc" type="boolean" value="false" truevalue="--skiprc" falsevalue="" label="Skip Reverse Complement" help="Skip checking of reverse complement sequences."/>
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56 <param name="gap_open" type="integer" value="1" label="Gap Open Penalty" help="Positive value of the gap open penalty."/>
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57 <param name="gap_extend" type="integer" value="1" label="Gap Extension Penalty" help="Positive value of the gap extension penalty."/>
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58 </when>
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59 <when value="score">
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60 <param argument="--start" type="integer" value="0" label="Start Position" help="The starting position of the primer."/>
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61 </when>
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62 </conditional>
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63 <param argument="--revpr" type="boolean" value="false" truevalue="--revpr" falsevalue="" label="Reverse Match" help="Match the reverse complement of primer sequences against the ends of reads."/>
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64 <param argument="--barcode" type="boolean" value="false" truevalue="--barcode" falsevalue="" label="Extract Barcodes (UMIs)" help="Capture the sequence preceding the primer as a UMI."/>
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65 <param argument="--maxerror" type="float" value="0.2" label="Max Error Rate" help="Maximum allowable rate between read and primer sequence."/>
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66 <expand macro="presto-log-param"/>
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67 </inputs>
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68
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69 <outputs>
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70 <data name="fastq_out" format="fastq" from_work_dir="tmp_mask_primers-pass.fastq"/>
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71 <expand macro="presto-log-output"/>
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72 </outputs>
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73
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74 <tests>
4
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75 <test expect_num_outputs="1">
0
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76 <param name="command" value="score"/>
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77 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/>
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78 <param name="start" value="0"/>
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79 <param name="primers_in" value="read1_primers.fasta"/>
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80 <param name="mode" value="cut"/>
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81 <param name="maxerror" value="0.15"/>
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82 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_score_out.fastq" sort="true"/>
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83 </test>
4
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84 <test expect_num_outputs="1">
0
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85 <param name="command" value="score"/>
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86 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/>
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87 <param name="start" value="17"/>
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88 <param name="barcode" value="true"/>
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89 <param name="primers_in" value="read2_primers.fasta"/>
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90 <param name="mode" value="cut"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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91 <param name="maxerror" value="0.15"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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92 <output name="fastq_out" file="presto_maskprimers_with_barcode_test_score_out.fastq" sort="true"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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93 </test>
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94 <test expect_num_outputs="1">
0
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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95 <param name="command" value="align"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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96 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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97 <param name="primers_in" value="read1_primers.fasta"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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98 <param name="mode" value="cut"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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99 <param name="maxerror" value="0.15"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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100 <param name="maxlen" value="25"/>
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101 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_align_out.fastq" sort="true"/>
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102 </test>
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103 <test expect_num_outputs="1">
0
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104 <param name="command" value="align"/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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105 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/>
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106 <param name="barcode" value="true"/>
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107 <param name="primers_in" value="read2_primers.fasta"/>
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108 <param name="mode" value="cut"/>
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109 <param name="maxerror" value="0.15"/>
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110 <param name="maxlen" value="25"/>
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111 <output name="fastq_out" file="presto_maskprimers_with_barcode_test_align_out.fastq" sort="true"/>
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112 </test>
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113 </tests>
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114
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115 <help><![CDATA[
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116 Removes primers and annotates sequences with primer and barcode identifiers
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117
1
61c1ae41a6bd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
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118 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
0
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119
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120 @HELP_NOTE@
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121 ]]></help>
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122 <expand macro="citations" />
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123 </tool>