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1 <tool id="sam_header" name="NGS Run Annotation">
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2 <description>Create a SAM format header from run metadata for sample annotation.</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.3">mimodd</requirement>
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5 </requirements>
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6 <command>
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7 mimodd header
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8
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9 --rg_id "$rg_id"
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10 --rg_sm "$rg_sm"
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11
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12 #if $str($rg_cn):
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13 --rg_cn "$rg_cn"
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14 #end if
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15 #if $str($rg_ds):
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16 --rg_ds "$rg_ds"
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17 #end if
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18 #if $str($anno) and $str($month) and $str($day):
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19 --rg_dt "$anno-$month-$day"
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20 #end if
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21 #if $str($rg_lb):
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22 --rg_lb "$rg_lb"
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23 #end if
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24 #if $str($rg_pl):
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25 --rg_pl "$rg_pl"
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26 #end if
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27 #if $str($rg_ds):
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28 --rg_pi "$rg_pi"
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29 #end if
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30 #if $str($rg_pu):
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31 --rg_pu "$rg_pu"
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32 #end if
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33
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34 --outputfile $outputfile
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35
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36 </command>
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37
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38 <inputs>
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39 <param name="rg_id" type="text" size="80" label="read-group ID (mandatory)">
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40 <sanitizer invalid_char="">
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41 <valid initial="string.printable">
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42 <remove value=""" />
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43 </valid>
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44 <mapping initial="none">
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45 <add source=""" target="\""/>
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46 </mapping>
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47 </sanitizer>
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48 </param>
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49 <param name="rg_sm" type="text" size="80" label="sample name (mandatory)">
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50 <sanitizer invalid_char="">
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51 <valid initial="string.printable">
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52 <remove value=""" />
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53 </valid>
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54 <mapping initial="none">
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55 <add source=""" target="\""/>
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56 </mapping>
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57 </sanitizer>
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58 </param>
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59 <param name="rg_cn" type="text" size="80" label="name of sequencing center">
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60 <sanitizer invalid_char="">
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61 <valid initial="string.printable">
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62 <remove value=""" />
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63 </valid>
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64 <mapping initial="none">
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65 <add source=""" target="\""/>
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66 </mapping>
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67 </sanitizer>
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68 </param>
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69 <param name="rg_ds" type="text" size="80" label="description">
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70 <sanitizer invalid_char="">
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71 <valid initial="string.printable">
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72 <remove value=""" />
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73 </valid>
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74 <mapping initial="none">
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75 <add source=""" target="\""/>
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76 </mapping>
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77 </sanitizer>
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78 </param>
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79 <param name="anno" type="text" label="year (YYYY) the run was produced" />
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80 <param name="month" type="text" label="month (MM) the run was produced" />
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81 <param name="day" type="text" label="day (DD) the run was produced" />
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82 <param name="rg_lb" type="text" size="80" label="read-group library">
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83 <sanitizer invalid_char="">
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84 <valid initial="string.printable">
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85 <remove value=""" />
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86 </valid>
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87 <mapping initial="none">
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88 <add source=""" target="\""/>
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89 </mapping>
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90 </sanitizer>
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91 </param>
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92 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" />
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93 <param name="rg_pi" type="text" label="predicted median insert size" />
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94 <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier">
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95 <sanitizer invalid_char="">
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96 <valid initial="string.printable">
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97 <remove value=""" />
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98 </valid>
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99 <mapping initial="none">
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100 <add source=""" target="\""/>
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101 </mapping>
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102 </sanitizer>
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103 </param>
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104 </inputs>
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105
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106 <outputs>
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107 <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/>
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108 </outputs>
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109
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110 <help>
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111 .. class:: infomark
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112
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113 **What it does**
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114
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115 This tool takes the user-provided information about a next-generation sequencing run and constructs a valid header in the SAM file format from it.
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116
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117 The result file can be used by the tools *Convert* and *Reheader* or in the *SNAP Read Alignment* step to add run metadata to sequenced reads files (or to overwrite pre-existing information).
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118
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119 **Note:**
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120
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121 **MiModD requires run metadata for every input file at the Alignment step !**
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122
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123 **Tip:**
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124
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125 While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, the **recommended approach** is to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming this practice protects against information loss and ensures that the input datasets will remain useful for others in the future.
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126
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127 </help>
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128 </tool>
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129
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