Mercurial > repos > iuc > colibread_takeabreak

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:54:32 +0000
parents 22a263a450d0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <macros>
5
8286fbe97349 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
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1339a2bb75ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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3 <token name="@PROFILE@">23.1</token>
6
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a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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5 <xml name="discosnp_requirements">
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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6 <requirements>
7
1339a2bb75ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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7 <requirement type="package" version="@TOOL_VERSION@">discosnp</requirement>
1
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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8 </requirements>
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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9 </xml>
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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11 <token name="@discosnp_single_for@"><![CDATA[
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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12 #for $input in $input_type_options.list_reads:
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13 ]]></token>
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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15 <token name="@discosnp_single_end_for@"><![CDATA[
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e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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16 echo '${filename}' >> input.lst &&
e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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17 #end for
e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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18 ]]></token>
1
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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20 <token name="@single_reads@"><![CDATA[
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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21 #import re
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22 #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
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23 #if $input.ext.startswith('fasta'):
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24 #set filename = $base_filename + ".fasta"
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25 #else:
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26 #set filename = $base_filename + ".fastq"
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27 #end if
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28 #if $input.ext.endswith('.gz'):
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29 gunzip -c '${input}' > '${filename}' &&
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30 #else:
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31 ln -sf '${input}' '${filename}' &&
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32 #end if
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33 ]]></token>
0
e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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34
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35 <token name="@discosnp_paired_for@"><![CDATA[
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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36 #for $i, $paired in enumerate($input_type_options.list_paired_reads):
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37 ]]></token>
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e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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6
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39 <token name="@discosnp_paired_end_for@"><![CDATA[
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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40 echo '${forward}' > "paired_${i}.lst" &&
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41 echo '${reverse}' >> "paired_${i}.lst" &&
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42 echo "paired_${i}.lst" >> input.lst &&
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43 #end for
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44 ]]></token>
0
e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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45
6
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46 <token name="@paired_reads@"><![CDATA[
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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47 #set $base_forward = re.sub('[^\w_]', '_', $paired.forward.element_identifier)
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48 #if $paired.forward.ext.startswith('fasta'):
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49 #set forward = $base_forward + ".fasta"
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50 #else:
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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51 #set forward = $base_forward + ".fastq"
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52 #end if
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53 #if $paired.forward.ext.endswith('.gz'):
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54 gunzip -c '$paired.forward' > '$forward' &&
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55 #else:
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56 ln -sf '${paired.forward}' '$forward' &&
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57 #end if
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58
6
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59 #set $base_reverse = re.sub('[^\w_]', '_', $paired.reverse.element_identifier)
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60 #if $paired.reverse.ext.startswith('fasta'):
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61 #set reverse = $base_reverse + ".fasta"
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62 #else:
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63 #set reverse = $base_reverse + ".fastq"
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64 #end if
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65 #if $paired.reverse.ext.endswith('.gz'):
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66 gunzip -c '$paired.reverse' > '$reverse' &&
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67 #else:
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68 ln -sf '${paired.reverse}' '$reverse' &&
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69 #end if
0
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70 ]]></token>
1
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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71
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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72 <xml name="discosnp_inputs">
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73 <conditional name="input_type_options">
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74 <param name="input_type" type="select" label="Input options">
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75 <option value="single">Single end reads</option>
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76 <option value="paired">Paired end reads</option>
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77 <option value="mix">Both single and paired reads</option>
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78 </param>
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79 <when value="single">
6
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80 <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
1
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81 </when>
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82 <when value="paired">
6
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83 <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
1
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84 </when>
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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85 <when value="mix">
6
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86 <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
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87 <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
1
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88 </when>
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89 </conditional>
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90 </xml>
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91
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92 <xml name="discosnp_options">
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93 <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/>
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94 <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/>
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95 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
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96 <param argument="-k" type="integer" label="Size of kmers" value="31" />
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97
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98 <conditional name="coverage_options_type" >
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99 <param name="coverage_options" type="select" label="Coverage option">
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100 <option value="auto"></option>
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101 <option value="custom"></option>
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102 </param>
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103 <when value="auto" />
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104 <when value="custom">
5
8286fbe97349 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
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105 <param argument="-c" type="text" label="Minimal coverage per read set" value="3" help="e.g. 3 / 3,5,17 / 3,auto,auto"/>
1
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106 </when>
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107 </conditional>
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108
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109 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
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110 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
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111
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112 </xml>
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113
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114 <token name="@discosnp_inputs@"><![CDATA[
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115 -r input.lst
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116 -D ${D}
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117 -P ${P}
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118 ${low_complexity}
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119 -k ${k}
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120
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121 #if str($coverage_options_type.coverage_options) == 'auto'
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122 -c auto
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123 #else
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124 -c '${coverage_options_type.c}'
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125 #end if
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126 -C ${C}
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127 -d ${d}
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128 ]]></token>
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129
0
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130 <token name="@lordec_inputs@"><![CDATA[
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131 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
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132 -i '${program_type_choice.i}'
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133 -k ${program_type_choice.k}
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134 -s ${program_type_choice.s}
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135 ]]></token>
1
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136
0
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137 <xml name="lordec_inputs">
6
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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138 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq,fastq.gz" multiple="true" label="Short read FASTA/Q files" />
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139 <param argument="-i" type="data" format="fasta,fastq.gz,fastq,fastq.gz" label="Long read FASTA/Q file" help="PacBio reads files" />
0
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140 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
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141 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
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142 </xml>
1
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143
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144 <token name="@discosnp_help@"><![CDATA[
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145 -------
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146
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147 .. class:: warningmark
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148
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149 **Input parameters**
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150
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151 -Sequences files in fasta or fastq each allele will be counted in each file individually
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152
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153 -Use collections: data list and/or data list paired
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154
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155 -Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
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156
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157 -------
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158
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159 .. class:: warningmark
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160
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161 **Ouput parameters**
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162
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163 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
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164
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165 -Fasta file with sequence extensions around the SNP.
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166
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167
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168 -------
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169
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170 **Web site**
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171
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172 https://colibread.inria.fr/software/discosnp/
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173
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174 ]]></token>
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175
0
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176 <xml name="citations">
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177 <citations>
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178 <yield/>
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179 <citation type="doi">10.1186/s13742-015-0105-2</citation>
e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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180 </citations>
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181 </xml>
1
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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182
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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183 <xml name="discosnp_citation">
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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184 <citation type="doi">10.1101/209965</citation>
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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185 </xml>
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186
0
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187 </macros>