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1 <tool id="alignreads" name="alignReads" version="0.0.1">
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2
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3 <description>alignReads: short read alignment tool wrapper</description>
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4 <requirements>
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5 <requirement type="package">trinity</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8
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9 trinityToolWrapper.py util/alignReads.pl --target $target -o alignment --aligner $aligner_selection.aligner
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10
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11
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12 ## Inputs.
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13 #if str($inputs.paired_or_single) == "paired":
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14 --left $inputs.left_input --right $inputs.right_input
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15 #if $inputs.left_input.ext == 'fa':
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16 --seqType fa
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17 #else:
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18 --seqType fq
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19 #end if
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20 #if str($inputs.library_type) != "None":
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21 --SS_lib_type $inputs.library_type
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22 #end if
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23 --max_dist_between_pairs $inputs.max_dist_between_pairs
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24 #else:
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25 --single $inputs.input
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26 #if str($inputs.input.ext) == 'fa':
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27 --seqType fa
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28 #else:
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29 --seqType fq
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30 #end if
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31 #if str($inputs.library_type) != "None":
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32 --SS_lib_type $inputs.library_type
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33 #end if
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34 #end if
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35
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36 ## Additional parameters.
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37 ##if str($inputs.use_additional) == "yes":
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38 ## -- $inputs.additional_params
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39 ##end if
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40
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41
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42 ## direct to output
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43 > outCapture.txt
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44
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45
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46 </command>
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47 <inputs>
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48 <param format="fasta" name="target" type="data" label="target" help="Fasta sequences targeted for short-read alignment" />
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49
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50 <conditional name="inputs">
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51 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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52 <option value="paired">Paired</option>
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53 <option value="single">Single</option>
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54 </param>
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55 <when value="paired">
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56 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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57 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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58 <param name="library_type" type="select" label="Strand-specific Library Type">
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59 <option value="None">None</option>
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60 <option value="FR">FR</option>
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61 <option value="RF">RF</option>
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62 </param>
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63 <param name="max_dist_between_pairs" type="integer" value="2000" min="1" label="max_dist_between_pairs" help="Maximum length expected between fragment pairs as aligned to the target, including introns where relevant."/>
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64
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65
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66 </when>
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67 <when value="single">
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68 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
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69 <param name="library_type" type="select" label="Strand-specific Library Type">
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70 <option value="None">None</option>
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71 <option value="F">F</option>
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72 <option value="R">R</option>
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73 </param>
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74 </when>
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75 </conditional>
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76
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77 <conditional name="aligner_selection">
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78 <param name="aligner" type="select" label="Select alignment tool to run">
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79 <option value="bowtie">bowtie</option>
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80 <option value="bwa">bwa</option>
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81 <option value="blat">blat</option>
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82 </param>
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83 <when value="blat">
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84 <param name="max_intron_length" type="integer" value="10000" min = "1" label="maximum intron length" help="" />
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85 <param name="min_percent_identity" type="integer" value="95" min="1" label="minimum percent identity" help="" />
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86 </when>
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87 <when value="bwa">
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88 </when>
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89 <when value="bowtie">
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90 </when>
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91 </conditional>
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92
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93
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94 <!--
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95 <conditional name="use_additional_params">
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96 <param name="use_additional" type="select" label="Use Additional Params?">
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97 <option value="no">No</option>
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98 <option value="yes">Yes</option>
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99 </param>
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100 <when value="no">
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101 </when>
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102 <when value="yes">
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103 <param name="additional_params" type="text" value="" label="Additional command-line parameters to aligner" help="" />
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104 </when>
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105 </conditional>
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106
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107 -->
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108
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109 </inputs>
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110 <outputs>
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111 <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: COORD-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>
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112 <data format="bam" name="nameSortedBam" label="${tool.name} on ${on_string}: NAME-sorted read alignments" from_work_dir="alignment/alignment.nameSorted.bam"/>
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113
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114 <!-- notes: need to retain:
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115 -the sample name for the alignment
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116 -coordinate-sorted vs. name-sorted bam file
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117 -paired vs. unpaired vs. strictly proper pairs (for RSEM)
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118 -strand-specific or not
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119 -->
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120
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121 </outputs>
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122 <tests>
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123
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124
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125 <test>
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126 <param name="target" value="trinity/Trinity.fasta" />
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127 <param name="aligner" value="bowtie" />
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128 <param name="paired_or_single" value="single" />
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129 <param name="library_type" value="None" />
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130 <param name="input" value="trinity/reads.left.fq" />
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131 </test>
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132
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133
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134 </tests>
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135 <help>
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136 .. _Trinity: http://trinityrnaseq.sourceforge.net
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137 </help>
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138 </tool>
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