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1 <tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.3">
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2 <description>Create a SAM format header from run metadata for sample annotation.</description>
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3 <macros>
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4 <import>toolshed_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>mimodd version -q</version_command>
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8 <command>
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9 mimodd header
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10
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11 --rg-id "$rg_id"
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12 --rg-sm "$rg_sm"
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13
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14 #if $str($rg_cn):
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15 --rg-cn "$rg_cn"
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16 #end if
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17 #if $str($rg_ds):
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18 --rg-ds "$rg_ds"
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19 #end if
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20 #if $str($rg_date):
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21 --rg-dt "$rg_date"
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22 #end if
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23 #if $str($rg_lb):
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24 --rg-lb "$rg_lb"
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25 #end if
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26 #if $str($rg_pl):
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27 --rg-pl "$rg_pl"
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28 #end if
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29 #if $str($rg_pi):
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30 --rg-pi "$rg_pi"
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31 #end if
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32 #if $str($rg_pu):
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33 --rg-pu "$rg_pu"
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34 #end if
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35
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36 --ofile "$outputfile"
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37
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38 </command>
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39
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40 <inputs>
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41 <param label="read-group ID (required)" name="rg_id" size="80" type="text">
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42 <sanitizer invalid_char="">
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43 <valid initial="string.printable">
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44 <remove value=""" />
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45 </valid>
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46 <mapping initial="none">
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47 <add source=""" target="\"" />
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48 </mapping>
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49 </sanitizer>
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50 </param>
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51 <param label="sample name (required)" name="rg_sm" size="80" type="text">
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52 <sanitizer invalid_char="">
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53 <valid initial="string.printable">
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54 <remove value=""" />
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55 </valid>
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56 <mapping initial="none">
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57 <add source=""" target="\"" />
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58 </mapping>
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59 </sanitizer>
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60 </param>
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61 <param label="description" name="rg_ds" size="80" type="text">
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62 <sanitizer invalid_char="">
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63 <valid initial="string.printable">
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64 <remove value=""" />
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65 </valid>
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66 <mapping initial="none">
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67 <add source=""" target="\"" />
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68 </mapping>
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69 </sanitizer>
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70 </param>
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71 <param label="date (YYYY-MM-DD) the run was produced" name="rg_date" type="text" />
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72 <param label="name of sequencing center" name="rg_cn" size="80" type="text">
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73 <sanitizer invalid_char="">
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74 <valid initial="string.printable">
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75 <remove value=""" />
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76 </valid>
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77 <mapping initial="none">
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78 <add source=""" target="\"" />
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79 </mapping>
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80 </sanitizer>
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81 </param>
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82 <param label="read-group library" name="rg_lb" size="80" type="text">
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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 label="platform/technology used to produce the reads" name="rg_pl" type="text" />
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93 <param label="predicted median insert size" name="rg_pi" type="text" />
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94 <param label="platform unit; unique identifier" name="rg_pu" size="80" type="text">
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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 format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}" name="outputfile" />
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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, 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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126
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127 </help>
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128 </tool>
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