Mercurial > repos > rnateam > mirdeep2_mapper

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 04c75332ac618b43ce5c3f307f7866e97147e865
author rnateam
date Thu, 05 Apr 2018 08:54:49 -0400
parents f844a9c1698d
children
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79fdac89dd6e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 04c75332ac618b43ce5c3f307f7866e97147e865
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1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0.8.1">
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2 <description>process and map reads to a reference genome</description>
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3 <macros>
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4 <macro name="map_params">
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5 <conditional name="refGenomeSource">
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6 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)">
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7 <option value="indexed">Use a built-in index</option>
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8 <option value="history">Use one from the history</option>
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9 </param>
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10 <when value="indexed">
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11 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin.">
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12 <options from_data_table="bowtie_indexes">
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13 <filter type="sort_by" column="2"/>
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14 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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15 </options>
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16 </param>
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17 </when> <!-- build-in -->
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18 <when value="history">
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19 <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />
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20 </when> <!-- history -->
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21 </conditional> <!-- refGenomeSource -->
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22 <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>
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23 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)">
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24 <validator type="in_range" min="1" message="Minimum value is 1"/>
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25 </param>
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26 </macro>
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27 </macros>
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28 <requirements>
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29 <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
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30 </requirements>
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31 <command detect_errors="aggressive">
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32 <![CDATA[
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33 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
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34 #if $operation.refGenomeSource.genomeSource == "history"
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35 bowtie-build '$operation.refGenomeSource.ownFile' custom_bowtie_indices &&
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36 #end if
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37 #end if
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38
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39 mapper.pl
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41 #if $input.type == "single":
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42 '$input.reads'
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44 #if $input.reads.extension.startswith("fasta")
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45 -c
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46 #else if $input.reads.extension.startswith("fastq")
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47 -e
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48 -h
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49 #end if
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50 #else:
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51 '$samples' -d
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53 #if $input.reads_list[0].reads.extension.startswith("fasta")
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54 -c
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55 #else if $input.reads_list[0].reads.extension.startswith("fastq")
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56 -e
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57 -h
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58 #end if
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59 #end if
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60
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61 $remove_non_canon
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62
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63 $convert_rna_dna
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64
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65 #if $clip_adapter.clip == "true"
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66 -k $clip_adapter.adapter_seq
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67 #end if
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68
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69 -l $discard_short_reads
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70
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71 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse"
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72 -m -s '$output_reads_collapsed'
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73 #end if
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74
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75 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
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76 -p
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77
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78 #if $operation.refGenomeSource.genomeSource == "history"
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79 custom_bowtie_indices
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80 #else
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81 '$operation.refGenomeSource.index.fields.path'
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82 #end if
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83 $operation.map_mismatch
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84 -r $operation.map_threshold
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85
2
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86 -t '$output_mapping'
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87 #end if
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88
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89 -v -n
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90 ]]>
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91 </command>
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92 <configfiles>
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93 <configfile name="samples"><![CDATA[#if $input.type == "multiple":
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94 #for $r in $input.reads_list:
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95 $r.reads $r.sample_name
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96 #end for
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97 #end if]]></configfile>
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98 </configfiles>
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99 <inputs>
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100 <conditional name="input">
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101 <param name="type" type="select" label="Pool multiple read sets">
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102 <option value="single" selected="true">No</option>
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103 <option value="multiple">Yes</option>
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104 </param>
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105 <when value="single">
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106 <param format="fastq,fasta" name="reads" type="data" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>
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107 </when>
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108 <when value="multiple">
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109 <repeat name="reads_list" title="Reads">
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110 <param name="sample_name" value="" type="text" label="Sample name" help="Must be a 3 letters/digits code">
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111 <validator type="expression" message="The sample name must be a 3 letters/digits code">len(value) == 3 and value.isalnum()</validator>
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112 </param>
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113 <param format="fastq,fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>
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114 </repeat>
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115 </when>
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116 </conditional>
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117 <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/>
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118 <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/>
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119
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120 <conditional name="clip_adapter">
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121 <param name="clip" type="select" label="Clip 3' Adapter Sequence" help="(-k)">
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122 <option value="false">Don't Clip</option>
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123 <option value="true">Clip Sequence</option>
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124 </param>
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125 <when value="true">
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126 <param name="adapter_seq" value="" type="text" optional="false" label="Sequence to clip" help="Adapter Sequence can only contain a,c,g,t,u,n,A,C,G,T,U,N">
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127 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator>
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128 </param>
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129 </when>
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130 <when value="false"/>
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131 </conditional>
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132
0
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133 <param name="discard_short_reads" value="18" type="integer" optional="false" label="Discard reads shorter than this length" help="Set to 0 to keep all reads. (-l)">
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134 <validator type="in_range" min="0" message="Minimum value is 0"/>
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135 </param>
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136
0
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137 <conditional name="operation">
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138 <param name="collapse_map" type="select" label="Collapse reads and/or Map" help="(-m) and/or (-p)">
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139 <option value="collapse_and_map">Collapse reads and Map</option>
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140 <option value="only_map">Map</option>
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141 <option value="only_collapse">Collapse</option>
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142 </param>
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143 <when value="collapse_and_map">
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144 <expand macro="map_params"/>
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145 </when>
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146 <when value="only_map">
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147 <expand macro="map_params"/>
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148 </when>
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149 <when value="only_collapse"/>
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150 </conditional>
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151 </inputs>
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152 <outputs>
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153 <data format="fasta" name="output_reads_collapsed" label="Collapsed reads of ${tool.name} on ${on_string}">
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154 <filter>
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155 (
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156 operation['collapse_map'] == "collapse_and_map" or
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157 operation['collapse_map'] == "only_collapse"
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158 )
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159 </filter>
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160 </data>
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161 <data format="tabular" name="output_mapping" label="Mapping output of ${tool.name} on ${on_string} in ARF format">
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162 <filter>
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163 (
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164 operation['collapse_map'] == "collapse_and_map" or
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165 operation['collapse_map'] == "only_map"
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166 )
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167 </filter>
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168 </data>
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169 </outputs>
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170 <tests>
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171 <test>
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172 <conditional name="input">
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173 <param name="type" value="single"/>
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174 <param name="reads" value="reads.fa"/>
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175 </conditional>
0
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176 <param name="remove_non_canon" value="True"/>
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177 <param name="clip" value="true"/>
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178 <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/>
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179 <param name="discard_short_reads" value="18"/>
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180 <param name="collapse_map" value="collapse_and_map"/>
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181 <param name="genomeSource" value="history"/>
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182 <param name="ownFile" value="cel_cluster.fa"/>
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183 <output name="output_reads_collapsed">
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184 <assert_contents>
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185 <has_text text=">seq_349713_x268"/>
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186 <has_text text="TCACCGGGTGTANATCAGCTAA"/>
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187 <has_text text=">seq_354255_x214"/>
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188 <has_text text="TAACCGGGTGAACACTTGCAGT"/>
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189 <has_text text=">seq_357284_x187"/>
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190 </assert_contents>
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191 </output>
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192 <output name="output_mapping">
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193 <assert_contents>
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194 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagcagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/>
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195 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagtagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/>
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196 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtgtacatcagcgaa\tchrII:11534525-11540624\t22\t3631\t3652.*$"/>
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197 <has_line_matching expression="^.*22\t1\t22\ttcaccgggagaaaaactggtgt\tchrII:11534525-11540624\t22\t3382\t3403.*$"/>
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198 <has_line_matching expression="^.*25\t1\t25\ttcaccgggtggaaactagcagtggc\tchrII:11534525-11540624\t25\t3060\t3084.*$"/>
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199 </assert_contents>
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200 </output>
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201 </test>
3
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202 <test>
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203 <conditional name="input">
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204 <param name="type" value="multiple"/>
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205 <repeat name="reads_list">
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206 <param name="sample_name" value="sa1"/>
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207 <param name="reads" value="reads_sample1.fa"/>
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208 </repeat>
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209 <repeat name="reads_list">
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210 <param name="sample_name" value="sa2"/>
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211 <param name="reads" value="reads_sample2.fa"/>
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212 </repeat>
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213 </conditional>
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214 <param name="remove_non_canon" value="True"/>
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215 <param name="clip" value="true"/>
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216 <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/>
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217 <param name="discard_short_reads" value="18"/>
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218 <param name="collapse_map" value="collapse_and_map"/>
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219 <param name="genomeSource" value="history"/>
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220 <param name="ownFile" value="cel_cluster.fa"/>
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221 <output name="output_reads_collapsed">
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222 <assert_contents>
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223 <has_text text=">sa1_220_x1"/>
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224 <has_text text="TCACCGGGTGTACATCAGC"/>
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225 <has_text text=">sa2_0_x250"/>
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226 <has_text text="AATGACACTGGTTATCTTTTCCATCG"/>
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227 </assert_contents>
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228 </output>
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229 <output name="output_mapping">
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230 <assert_contents>
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231 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagcagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/>
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232 <has_line_matching expression="^.*21\t1\t21\ttcaccgggtggaaactagcag\tchrII:11534525-11540624\t21\t3060\t3080.*$"/>
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233 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtgtacatcagctaa\tchrII:11534525-11540624\t22\t3631\t3652.*$"/>
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234 </assert_contents>
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235 </output>
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236 </test>
0
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237 </tests>
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238 <help>
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239 <![CDATA[
2
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240 **What it does**
0
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241
3
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242 The MiRDeep2 Mapper module is designed as a tool to process deep sequencing reads and/or map them to the reference genome.
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243 The module works in sequence space, and can process or map data that is in sequence FASTA format.
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244 A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind.
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245
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246 **Input**
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247
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248 Default input is a file in FASTA format, seq.txt or qseq.txt format. More input can be given depending on the options used.
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249
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250 **Output**
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251
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252 The output depends on the options used. Either a FASTA file with processed reads or an arf file with with mapped reads, or both, are output.
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253
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254 Arf format:
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255 Is a proprietary file format generated and processed by miRDeep2. It contains information of reads mapped to a reference genome. Each line in such a file contains 13 columns:
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256
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257 1. read identifier
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258 2. length of read sequence
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259 3. start position in read sequence that is mapped
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260 4. end position in read sequence that is mapped
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261 5. read sequence
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262 6. identifier of the genome-part to which a read is mapped to. This is either a scaffold id or a chromosome name
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263 7. length of the genome sequence a read is mapped to
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264 8. start position in the genome where a read is mapped to
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265 9. end position in the genome where a read is mapped to
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266 10. genome sequence to which a read is mapped
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267 11. genome strand information. Plus means the read is aligned to the sense-strand of the genome. Minus means it is aligned to the antisense-strand of the genome.
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268 12. Number of mismatches in the read mapping
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269 13. Edit string that indicates matches by lowercase 'm' and mismatches by uppercase 'M'
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270
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271 ]]>
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272 </help>
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273 <citations>
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274 <citation type="doi">10.1093/nar/gkr688</citation>
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275 <citation type="doi">10.1002/0471250953.bi1210s36</citation>
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276 </citations>
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277 </tool>