Mercurial > repos > iuc > presto_filterseq

annotate presto_filterseq.xml @ 5:3c0bc20253b4 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 08:58:53 +0000
parents 56e5741103bb
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56e5741103bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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1 <tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description>
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3 <macros>
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4 <import>presto_macros.xml</import>
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5 </macros>
5
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6 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9
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10 <version_command>FilterSeq.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
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13 FilterSeq.py '$cc.command'
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14 --nproc "\${GALAXY_SLOTS:-1}"
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15 -s in.fastq
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16 #if $varExists('cc.q')
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17 -q '$cc.q'
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18 #end if
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19 #if $getVar('cc.inner', False)
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20 --inner
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21 #end if
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22 #if $varExists('cc.win')
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23 --win '$cc.win'
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24 #end if
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25 #if $getVar('cc.reverse', False)
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26 --reverse
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27 #end if
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28 #if $varExists('cc.n')
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29 -n '$cc.n'
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30 #end if
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31 --outdir=.
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32 --outname=tmp_filter_seq
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33 #if $capture_log
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34 --log '$log_out'
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35 #end if
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36 &&
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37 mv ./tmp_filter_seq_${cc.command}-pass.fastq $fastq_out
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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 <conditional name="cc">
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42 <param name="command" type="select" label="Command">
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43 <option value="length">Filters reads by length (length)</option>
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44 <option value="missing">Filters reads by N or gap character count (missing)</option>
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45 <option value="repeats">Filters reads by consecutive nucleotide repeats (repeats)</option>
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46 <option value="quality">Filters reads by quality score (quality)</option>
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47 <option value="maskqual">Masks low quality positions (maskqual)</option>
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48 <option value="trimqual">Trims sequences by quality score decay (trimqual)</option>
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49 </param>
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50 <when value="length">
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51 <param argument="-n" type="integer" value="" label="Minimum Length" help="Discard reads shorter than this number of bases long."/>
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52 </when>
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53 <when value="missing">
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54 <param argument="-n" type="integer" value="" label="Max Missing" help="Dicard reads with more than this many no-calls or gaps."/>
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55 </when>
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56 <when value="repeats">
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57 <param argument="-n" type="integer" value="" label="Max Repeat Length" help="Discard reads with simple repeats of this length of longer."/>
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58 </when>
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59 <when value="quality">
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60 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
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61 <param argument="--inner" type="boolean" value="false" label="End-Trim Ns" help="Exclude Ns at the ends of the reads from calculation."/>
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62 </when>
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63 <when value="maskqual">
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64 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
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65 </when>
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66 <when value="trimqual">
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67 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
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68 <param argument="--win" type="integer" value="10" label="Window Size" help="Window size for moving average quality calculation."/>
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69 <param argument="--reverse" type="boolean" value="false" label="Reverse" help="If true trim the start of the reads instead of the ends."/>
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70 </when>
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71 </conditional>
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72 <expand macro="presto-log-param"/>
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73 </inputs>
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74
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75 <outputs>
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76 <data name="fastq_out" format="fastq"/>
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77 <expand macro="presto-log-output"/>
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78 </outputs>
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79
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80 <tests>
5
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81 <test expect_num_outputs="1">
0
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82 <param name="command" value="length"/>
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83 <param name="n" value="299"/>
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84 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
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85 <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/>
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86 </test>
5
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87 <test expect_num_outputs="1">
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88 <param name="command" value="missing"/>
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89 <param name="n" value="281"/>
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90 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
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91 <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/>
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92 </test>
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93 <test expect_num_outputs="1">
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94 <param name="command" value="repeats"/>
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95 <param name="n" value="8"/>
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96 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
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97 <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/>
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98 </test>
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99 <test expect_num_outputs="1">
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100 <param name="command" value="quality"/>
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101 <param name="q" value="30"/>
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102 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
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103 <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/>
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104 </test>
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105 <test expect_num_outputs="1">
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106 <param name="command" value="maskqual"/>
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107 <param name="q" value="30"/>
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108 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
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109 <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/>
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110 </test>
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111 <test expect_num_outputs="1">
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112 <param name="command" value="trimqual"/>
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113 <param name="q" value="30"/>
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114 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
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115 <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/>
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116 </test>
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117 </tests>
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118
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119 <help><![CDATA[
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120 Filters and/or masks reads based on length, quality, missing bases and repeats.
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121
1
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122 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
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123
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124 @HELP_NOTE@
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125 ]]></help>
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126 <expand macro="citations" />
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127 </tool>