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1 <tool id="ngs_run_annotation" 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="0.1.5">mimodd</requirement>
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5 </requirements>
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6 <version_command>mimodd version -q</version_command>
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7 <command>
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8 mimodd header
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9
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10 --rg-id "$rg_id"
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11 --rg-sm "$rg_sm"
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12
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13 #if $str($rg_cn):
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14 --rg-cn "$rg_cn"
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15 #end if
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16 #if $str($rg_ds):
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17 --rg-ds "$rg_ds"
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18 #end if
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19 #if $str($rg_date):
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20 --rg-dt "$rg_date"
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21 #end if
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22 #if $str($rg_lb):
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23 --rg-lb "$rg_lb"
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24 #end if
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25 #if $str($rg_pl):
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26 --rg-pl "$rg_pl"
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27 #end if
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28 #if $str($rg_pi):
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29 --rg-pi "$rg_pi"
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30 #end if
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31 #if $str($rg_pu):
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32 --rg-pu "$rg_pu"
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33 #end if
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34
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35 --ofile $outputfile
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36
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37 </command>
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38
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39 <inputs>
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40 <param name="rg_id" type="text" size="80" label="read-group ID (required)">
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41 <sanitizer invalid_char="">
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42 <valid initial="string.printable">
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43 <remove value=""" />
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44 </valid>
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45 <mapping initial="none">
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46 <add source=""" target="\""/>
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47 </mapping>
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48 </sanitizer>
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49 </param>
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50 <param name="rg_sm" type="text" size="80" label="sample name (required)">
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51 <sanitizer invalid_char="">
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52 <valid initial="string.printable">
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53 <remove value=""" />
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54 </valid>
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55 <mapping initial="none">
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56 <add source=""" target="\""/>
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57 </mapping>
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58 </sanitizer>
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59 </param>
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60 <param name="rg_ds" type="text" size="80" label="description">
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61 <sanitizer invalid_char="">
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62 <valid initial="string.printable">
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63 <remove value=""" />
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64 </valid>
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65 <mapping initial="none">
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66 <add source=""" target="\""/>
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67 </mapping>
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68 </sanitizer>
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69 </param>
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70 <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" />
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71 <param name="rg_cn" type="text" size="80" label="name of sequencing center">
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72 <sanitizer invalid_char="">
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73 <valid initial="string.printable">
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74 <remove value=""" />
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75 </valid>
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76 <mapping initial="none">
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77 <add source=""" target="\""/>
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78 </mapping>
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79 </sanitizer>
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80 </param>
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81 <param name="rg_lb" type="text" size="80" label="read-group library">
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82 <sanitizer invalid_char="">
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83 <valid initial="string.printable">
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84 <remove value=""" />
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85 </valid>
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86 <mapping initial="none">
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87 <add source=""" target="\""/>
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88 </mapping>
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89 </sanitizer>
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90 </param>
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91 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" />
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92 <param name="rg_pi" type="text" label="predicted median insert size" />
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93 <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier">
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94 <sanitizer invalid_char="">
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95 <valid initial="string.printable">
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96 <remove value=""" />
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97 </valid>
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98 <mapping initial="none">
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99 <add source=""" target="\""/>
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100 </mapping>
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101 </sanitizer>
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102 </param>
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103 </inputs>
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104
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105 <outputs>
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106 <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/>
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107 </outputs>
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108
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109 <help>
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110 .. class:: infomark
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111
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112 **What it does**
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113
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114 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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115
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116 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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117
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118 **Note:**
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119
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120 **MiModD requires run metadata for every input file at the Alignment step !**
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121
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122 **Tip:**
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123
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124 While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, we **recommend** you 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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125
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126 </help>
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127 </tool>
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128
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