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1 <tool id="Stampy" name="Stampy" version="1.0.21">
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2 <description>is a package for mapping of short reads from illumina sequencing machines onto a reference genome</description>
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3 <command interpreter="python"> stampy_wrapper.py
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4
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5 ## Indexing of the reference genome
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6 --assembly=$Assembly
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7 --species=$species
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8 --genome_index=$G
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9 --output=$output
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10
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11 ## Reference genome for creating index
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12 --genome=$input
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13 #if $refGenomeSource.genomeSource == "indexed":
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14 --genome1="${refGenomeSource.index.fields.path}"
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15 #end if
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16 ## input file for single paired read
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17 --input1=$input1
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18
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19 ## Second input only if input is paired-end.
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20 #if $singlePaired.sPaired == "paired"
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21 --input1=$singlePaired.input1
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22 --input2=$singlePaired.input2
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23 #end if
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24 ## Parameters
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25 --settings=$params.settingsType
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26 #if $params.settingsType == "full":
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27 --sd=${params.d}
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28 --insert=${params.i}
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29 --subrate=${params.r}
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30 #end if
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31 </command>
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32 <inputs>
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33 <param name="Assembly" type="text" value=""/>
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34 <param name="species" type="text" value=""/>
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35 <param name="G" type="text" value=""/>
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36
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37 <conditional name="refGenomeSource">
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38 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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39 <option value="indexed">Use a built-in index</option>
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40 <option value="history" selected="true">Use one from the history</option>
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41 </param>
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42 <when value="indexed">
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43 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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44 <options from_file="stampy_indices.loc">
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45 <column name ="value" index="0" />
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46 <column name ="name" index="1" />
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47 </options>
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48 </param>
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49 </when>
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50 <when value="history">hg18_
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51 <param name="input" type="data" format="fna" metadata_name="dbkey" label="Select the reference genome" />
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52 </when>
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53
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54 </conditional>
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55 <conditional name="singlePaired">
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56 <param name="sPaired" type="select" label="Is this library mate-paired?">
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57 <option value="single">Single-end</option>
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58 <option value="paired">Paired-end</option>
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59 </param>
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60 <when value="single">
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61 <param format="fna" name="input1" type="data" label="Input sequence" />
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62 </when>
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63 <when value="paired">
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64 <param format="fna" name="input1" type="data" label="Input sequence" />
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65 <param format="fna" name="input2" type="data" label="Input sequence" />
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66 </when>
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67 </conditional>
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68 <conditional name="params">
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69 <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
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70 <option value="preSet">Use Defaults</option>
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71 <option value="full">Full parameter list</option>
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72 </param>
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73 <when value="preSet" />
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74 <!-- Full/advanced parameters. -->
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75 <when value="full">
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76 <param name="i" type="text" value="250" label="Insert size" />
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77 <param name="d" type="text" value="50" label="standard deviation" />
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78 <param name="r" type="text" value="0.001" label="substitutionrate" />
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79 </when> <!-- full -->
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80 </conditional> <!-- params -->
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81
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82 </inputs>
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83
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84 <outputs>
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85 <data format="txt" name="output" label="outfile"/>
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86 </outputs>
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87 <help>
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88 **Stampy**
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89
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90 Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome (http://www.well.ox.ac.uk/project-stampy). Selected options used here are given below
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91
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92 ------
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93
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94 **Indexing usage**
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95
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96 *Building index*
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97
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98 stampy.py --species=human --assembly=hg18_ncbi36 -G hg18 /data/genomes/hg18/*.fa.gz
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99
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100 *Building hash*
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101
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102 stampy.py -g hg18 -H hg18
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103
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104 ------
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105
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106
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107 **Alignment usage**
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108
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109 stampy.py options -g hg18 -h hg18 -M reads_1.fastq reads_2.fastq
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110
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111
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112 ------
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113
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114 **Options - Description**
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115
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116 --insertsize
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117
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118 Set the mean insert size for paired-end reads (default: 250)
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119
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120 --insertsd=N
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121
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122 Set the standard deviation of the insert size distribution (default: 60)
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123
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124 --substitutionrate=S
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125
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126 Introduce an expected fraction S of Poisson-distributed substitutions (default: 0.001)
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127
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128
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129 </help>
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130
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131 </tool>
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132
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