Mercurial > repos > iuc > colibread_takeabreak

annotate macros.xml @ 6:22a263a450d0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author iuc
date Thu, 06 May 2021 12:46:24 +0000
parents 8286fbe97349
children 1339a2bb75ce
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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
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2 <token name="@DISCOSNP_VERSION@">2.5.4</token>
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4 <token name="@PROFILE@">20.01</token>
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6 <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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7 <requirements>
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8 <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
1
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9 </requirements>
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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10 </xml>
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12 <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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13 #for $input in $input_type_options.list_reads:
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14 ]]></token>
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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16 <token name="@discosnp_single_end_for@"><![CDATA[
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e1fdaacdabc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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17 echo '${filename}' >> input.lst &&
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18 #end for
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19 ]]></token>
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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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21 <token name="@single_reads@"><![CDATA[
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22 #import re
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23 #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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24 #if $input.ext.startswith('fasta'):
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25 #set filename = $base_filename + ".fasta"
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26 #else:
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27 #set filename = $base_filename + ".fastq"
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28 #end if
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29 #if $input.ext.endswith('.gz'):
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30 gunzip -c '${input}' > '${filename}' &&
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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31 #else:
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32 ln -sf '${input}' '${filename}' &&
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33 #end if
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34 ]]></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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36 <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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37 #for $i, $paired in enumerate($input_type_options.list_paired_reads):
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38 ]]></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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40 <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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41 echo '${forward}' > "paired_${i}.lst" &&
22a263a450d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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42 echo '${reverse}' >> "paired_${i}.lst" &&
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43 echo "paired_${i}.lst" >> input.lst &&
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44 #end for
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45 ]]></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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47 <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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48 #set $base_forward = re.sub('[^\w_]', '_', $paired.forward.element_identifier)
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49 #if $paired.forward.ext.startswith('fasta'):
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50 #set forward = $base_forward + ".fasta"
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51 #else:
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52 #set forward = $base_forward + ".fastq"
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53 #end if
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54 #if $paired.forward.ext.endswith('.gz'):
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55 gunzip -c '$paired.forward' > '$forward' &&
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56 #else:
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57 ln -sf '${paired.forward}' '$forward' &&
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58 #end if
0
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59
6
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60 #set $base_reverse = re.sub('[^\w_]', '_', $paired.reverse.element_identifier)
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61 #if $paired.reverse.ext.startswith('fasta'):
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62 #set reverse = $base_reverse + ".fasta"
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63 #else:
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64 #set reverse = $base_reverse + ".fastq"
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65 #end if
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66 #if $paired.reverse.ext.endswith('.gz'):
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67 gunzip -c '$paired.reverse' > '$reverse' &&
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68 #else:
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69 ln -sf '${paired.reverse}' '$reverse' &&
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70 #end if
0
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71 ]]></token>
1
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72
a018b8f663ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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73 <xml name="discosnp_inputs">
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74 <conditional name="input_type_options">
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75 <param name="input_type" type="select" label="Input options">
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76 <option value="single">Single end reads</option>
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77 <option value="paired">Paired end reads</option>
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78 <option value="mix">Both single and paired reads</option>
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79 </param>
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80 <when value="single">
6
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81 <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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82 </when>
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83 <when value="paired">
6
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84 <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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85 </when>
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86 <when value="mix">
6
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87 <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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88 <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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89 </when>
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90 </conditional>
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91 </xml>
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92
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93 <xml name="discosnp_options">
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94 <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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95 <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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96 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
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97 <param argument="-k" type="integer" label="Size of kmers" value="31" />
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98
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99 <conditional name="coverage_options_type" >
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100 <param name="coverage_options" type="select" label="Coverage option">
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101 <option value="auto"></option>
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102 <option value="custom"></option>
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103 </param>
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104 <when value="auto" />
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105 <when value="custom">
5
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106 <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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107 </when>
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108 </conditional>
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109
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110 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
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111 <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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112
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113 </xml>
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114
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115 <token name="@discosnp_inputs@"><![CDATA[
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116 -r input.lst
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117 -D ${D}
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118 -P ${P}
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119 ${low_complexity}
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120 -k ${k}
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121
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122 #if str($coverage_options_type.coverage_options) == 'auto'
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123 -c auto
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124 #else
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125 -c '${coverage_options_type.c}'
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126 #end if
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127 -C ${C}
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128 -d ${d}
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129 ]]></token>
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130
0
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131 <token name="@lordec_inputs@"><![CDATA[
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132 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
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133 -i '${program_type_choice.i}'
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134 -k ${program_type_choice.k}
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135 -s ${program_type_choice.s}
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136 ]]></token>
1
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137
0
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138 <xml name="lordec_inputs">
6
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139 <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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140 <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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141 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
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142 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
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143 </xml>
1
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144
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145 <token name="@discosnp_help@"><![CDATA[
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146 -------
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147
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148 .. class:: warningmark
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149
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150 **Input parameters**
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151
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152 -Sequences files in fasta or fastq each allele will be counted in each file individually
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153
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154 -Use collections: data list and/or data list paired
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155
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156 -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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157
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158 -------
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159
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160 .. class:: warningmark
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161
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162 **Ouput parameters**
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163
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164 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
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165
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166 -Fasta file with sequence extensions around the SNP.
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167
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168
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169 -------
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170
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171 **Web site**
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172
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173 https://colibread.inria.fr/software/discosnp/
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174
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175 ]]></token>
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176
0
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177 <xml name="citations">
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178 <citations>
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179 <yield/>
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180 <citation type="doi">10.1186/s13742-015-0105-2</citation>
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181 </citations>
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182 </xml>
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183
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184 <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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185 <citation type="doi">10.1101/209965</citation>
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186 </xml>
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187
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188 </macros>