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1 <tool id="bsfcall" name="bsfcall" version="1.0.0">
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0
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2 <description>Mapping bisulfite-seq reads and calling methylated cytosines</description>
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3 <!--
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4 <version_command></version_command>
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5 -->
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6
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7 <requirements>
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8 <requirement type="set_environment">TOOLDIR</requirement>
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9 </requirements>
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10
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11 <command interpreter="perl">
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1
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12 bsfcall_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1}
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13
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14 #if $reference.source=="indexed":
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15 $reference.index.fields.path
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16 #else if $reference.source=="history":
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17 $reference.own_file
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18 #else
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19
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20 #end if
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21
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22 #if $read.end=="single-end"
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23 $in
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24 #else if $read.end=="paired-end"
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25 $in1 $in2
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26 #else
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27
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28 #end if
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29 </command>
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30
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31 <inputs>
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32 <conditional name="reference">
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33 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
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34 <option value="indexed">Use a built-in genome index</option>
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35 <option value="history">Use a genome from the history and build index</option>
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36 </param>
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37 <when value="indexed">
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38 <param name="index" type="select" label="Select reference genome">
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39 <options from_data_table="bsfcall_indexes">
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40 <filter type="sort_by" column="2"/>
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41 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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42 </options>
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="own_file" type="data" format="fasta" label="Select reference genome"/>
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47 </when>
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48 </conditional>
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49
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50 <conditional name="read">
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51 <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
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52 <option value="single-end">Single-end reads</option>
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53 <option value="paired-end">Paired-end reads</option>
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54 </param>
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55 <when value="single-end">
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56 <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
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57 </when>
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58 <when value="paired-end">
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59 <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
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60 <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
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61 </when>
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62 </conditional>
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63 </inputs>
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64
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65 <outputs>
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66 <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/>
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67 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/>
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68 </outputs>
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69
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70 <help>
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71 **bsf-call**
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72
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73 Mapping bisulfite-seq reads and calling methylated cytosines
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74
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75 ------
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76
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77 **Input format**
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78
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79 Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file).
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80
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81 ------
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82
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83 **Output format**
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84
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85 Output is a six-column tab-delimited file::
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86
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87 Col.| Description
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88 ----+--------------------------------------
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89 1 | chromosome label (e.g. chr1)
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90 2 | genomic position (0-based)
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91 3 | strand (+,-)
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92 4 | mC context (CG, CHG, CHH)
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93 5 | mC rate (float)
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94 6 | read coverage
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95
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96 ------
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97
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98 **Contact**
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99
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100 Toutai Mituyama
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101
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102 mituyama-toutai AT aist.go.jp
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103 </help>
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104
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105 <citations>
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106 <citation type="doi">10.1093/nar/gkt1373</citation>
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107 </citations>
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108
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109 </tool>
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110
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111 <!--
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112 Also note the use of the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data directory.
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113 \${GALAXY_SLOTS:-4}
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114
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115 Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime).
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116 -->
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