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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
author wolma
date Sat, 11 Nov 2017 16:39:44 -0500
parents 85576338fbcf
children
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85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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1 <tool id="mimodd_reheader" name="MiModD Reheader" version="@MIMODD_WRAPPER_VERSION@">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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2 <description>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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3 takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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4 </description>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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5 <macros>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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6 <import>macros.xml</import>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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7 <macro name="getreadgroupinfo">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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8 <conditional name="rginfo">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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9 <param name="source" type="select"
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10 label="source of new read-group information">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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11 <option value="from_file">existing SAM file</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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12 <option value="from_form">input form</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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13 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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14 <when value="from_file">
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15 <param name="data" type="data" format="sam"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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16 label="read-group template file in SAM format"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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17 help="use the read group information found in this file" />
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18 <repeat name="rg" title="custom read-group mapping" default="0" min="0"
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19 help="read-group information found in the input file, by default, gets updated / replaced with information from template file read-groups with matching IDs. Alternatively, you may specify explicit read-group mappings below.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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20 <param name="source_id" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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21 label="modify input file information for read-group ID (will create the read-group if it does not exist)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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22 <param name="rg_id" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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23 label="with template file information for read-group ID" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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24 </repeat>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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25 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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26 <when value="from_form">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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27 <repeat name="rg" title="new read-group info" default="1" min="1">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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28 <param name="source_id" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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29 label="read-group ID (will create the read-group if it does not exist)"
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30 help="required field">
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31 <validator type="empty_field" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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32 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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33 <param name="rg_id" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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34 <param name="rg_sm" type="text" label="sample name"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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35 help="required field">
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36 <validator type="empty_field" />
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37 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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38 <param name="rg_ds" type="text" label="description" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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39 <param name="rg_date" type="text"
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40 label="date (YY-MM-DD format) the run was produced" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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41 <param name="rg_cn" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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42 label="name of sequencing center" />
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43 <param name="rg_lb" type="text" label="read-group library" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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44 <param name="rg_pl" type="text"
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45 label="platform/technology used to produce the reads" />
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46 <param name="rg_pi" type="text"
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47 label="predicted median insert size" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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48 <param name="rg_pu" type="text"
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49 label="platform unit; unique identifier" />
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50 </repeat>
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51 </when>
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52 </conditional>
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53 </macro>
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54 </macros>
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55 <expand macro="requirements" />
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56 <expand macro="stdio" />
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57 <expand macro="version_command" />
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58 <command><![CDATA[
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59 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
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60 mimodd header
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61 #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form":
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62 #for $rginfo in $rg.rginfo.rg
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63 #if $str($rginfo.source_id):
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64 --rg-id '${rginfo.source_id}'
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65 #end if
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66 #if $str($rginfo.rg_sm):
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67 --rg-sm '${rginfo.rg_sm}'
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68 #end if
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69 #if $str($rginfo.rg_cn):
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70 --rg-cn '${rginfo.rg_cn}'
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71 #else:
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72 --rg-cn ""
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73 #end if
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74 #if $str($rginfo.rg_ds):
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75 --rg-ds '${rginfo.rg_ds}'
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76 #else:
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77 --rg-ds ""
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78 #end if
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79 #if $str($rginfo.rg_date):
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80 --rg-dt '${rginfo.rg_date}'
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81 #else:
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82 --rg-dt ""
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83 #end if
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84 #if $str($rginfo.rg_lb):
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85 --rg-lb '${rginfo.rg_lb}'
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86 #else:
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87 --rg-lb ""
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88 #end if
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89 #if $str($rginfo.rg_pl):
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90 --rg-pl '${rginfo.rg_pl}'
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91 #else:
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92 --rg-pl ""
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93 #end if
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94 #if $str($rginfo.rg_pi):
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95 --rg-pi '${rginfo.rg_pi}'
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96 #else:
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97 --rg-pi ""
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98 #end if
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99 #if $str($rginfo.rg_pu):
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100 --rg-pu '${rginfo.rg_pu}'
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101 #else:
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102 --rg-pu ""
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103 #end if
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104 #end for
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105 #end if
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106 #if $str($co.treat_co) != "ignore":
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107 --co
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108 #for $comment in $co.coinfo
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109 #if $str($comment.line):
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110 '${comment.line}'
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111 #end if
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112 #end for
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113 #end if
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114 |
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115 #end if
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116 mimodd reheader '$inputfile' --sq ignore --rg ${rg.treat_rg}
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117 #if $str($rg.treat_rg) != "ignore":
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118 #if $str($rg.rginfo.source) == "from_file":
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119 '${rg.rginfo.data}'
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120 #else:
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121 -
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122 #end if
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123 #for $rgmapping in $rg.rginfo.rg
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124 #if $str($rgmapping.source_id) and $str($rgmapping.rg_id):
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125 '$str($rgmapping.source_id)' : '$str($rgmapping.rg_id)'
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126 #end if
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127 #end for
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128 #end if
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129
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130 --co ${co.treat_co}
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131 #if $str($co.treat_co) != "ignore":
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132 -
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133 #end if
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134
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135 #set $restr = ""
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136 #for $rename in $rg_renaming
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137 #set $restr = $restr + ($str($rename.from) and $str($rename.to) and "'" + $str($rename.from) + "' : '" + $str($rename.to) + "' ")
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138 #end for
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139 #if $restr
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140 --rgm $restr
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141 #end if
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142
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143 #set $restr = ""
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144 #for $rename in $sq_renaming
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145 #set $restr = $restr + ($str($rename.from) and $str($rename.to) and "'" + $str($rename.from) + "' : '" + $str($rename.to) + "' ")
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146 #end for
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147 #if $restr
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148 --sqm $restr
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149 #end if
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150
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151 -o '$output'
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152 ]]></command>
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153
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154 <inputs>
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155 <param name="inputfile" type="data" format="bam"
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156 label="input dataset in BAM format" help="the file to reheader." />
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157 <conditional name="rg">
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158 <param name="treat_rg" type="select"
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159 label="modify read-group information?"
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160 help="Replace mode will ignore ALL existing read group information in the input file and use ONLY template information, Update mode will COPY existing input file information and UPDATE it with template information; choose No, ... to leave read-group information alone.">
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161 <option value="ignore">No, do not change read-groups.</option>
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162 <option value="update">Yes, update existing information</option>
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163 <option value="replace">Yes, replace existing information</option>
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164 </param>
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165 <when value="update">
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166 <expand macro="getreadgroupinfo" />
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167 </when>
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168 <when value="replace">
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169 <expand macro="getreadgroupinfo" />
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170 </when>
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171 <when value="ignore">
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172 </when>
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173 </conditional>
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174 <conditional name="co">
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175 <param name="treat_co" type="select"
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176 label="modify comments in the input file?">
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177 <option value="ignore">No, do not change comments.</option>
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178 <option value="update">Yes, append new comments to existing ones</option>
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179 <option value="replace">Yes, replace all existing comments</option>
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180 </param>
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181 <when value="update">
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182 <repeat name="coinfo" title="comment line" default="0" min="0">
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183 <param name="line" type="text" size="80" />
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184 </repeat>
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185 </when>
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186 <when value="replace">
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187 <repeat name="coinfo" title="comment line" default="0" min="0">
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188 <param name="line" type="text" size="80" />
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189 </repeat>
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190 </when>
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191 <when value="ignore">
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192 </when>
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193 </conditional>
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194 <repeat name="rg_renaming" title="rename read-group" default="0" min="0"
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195 help="Warning: changing read-group IDs may increase job runtime substantially.">
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196 <param name="from" type="text" size="30" label="old name"
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197 help="as it appears in the current input file header"/>
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198 <param name="to" type="text" size="30" label="new name" />
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199 </repeat>
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200 <repeat name="sq_renaming" title="rename sequence" default="0" min="0"
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201 help="Warning: changing sequence names may increase job runtime substantially.">
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202 <param name="from" type="text" size="30" label="old name"
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203 help="as it appears in the current input file header"/>
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204 <param name="to" type="text" size="30" label="new name" />
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205 </repeat>
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206 </inputs>
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207
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208 <outputs>
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209 <data name="output" format="bam"
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210 label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}" />
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211 </outputs>
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212
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213 <tests>
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214 <test>
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215 <param name="inputfile" value="a.bam" />
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216 <conditional name="co">
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217 <param name="treat_co" value="update" />
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218 <repeat name="coinfo">
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219 <param name="line" value="ceterum censeo ..." />
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220 </repeat>
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221 </conditional>
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222 <output name="output" file="a.bam" ftype="bam" lines_diff="1" />
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223 </test>
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224 <test>
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225 <param name="inputfile" value="header_only.bam" />
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226 <conditional name="rg">
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227 <param name="treat_rg" value="update" />
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228 <conditional name="rginfo">
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229 <param name="source" value="from_form" />
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230 <repeat name="rg">
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231 <param name="source_id" value="000" />
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232 <param name="rg_sm" value="Bristol" />
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233 </repeat>
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234 </conditional>
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235 </conditional>
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236 <output name="output" file="header_only.bam" ftype="bam" lines_diff="2" />
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237 </test>
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238 <test>
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239 <param name="inputfile" value="header_only.bam" />
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240 <conditional name="rg">
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241 <param name="treat_rg" value="update" />
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242 <conditional name="rginfo">
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243 <param name="source" value="from_form" />
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244 <repeat name="rg">
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245 <param name="source_id" value="001" />
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246 <param name="rg_sm" value="Hawaiian" />
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247 </repeat>
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248 </conditional>
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249 </conditional>
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250 <output name="output" file="header_only.bam" ftype="bam" lines_diff="1" />
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251 </test>
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252 </tests>
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253
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254 <help><![CDATA[
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255 .. class:: infomark
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256
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257 **What it does**
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258
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259 The tool generates a copy of the BAM input file with a modified header (i.e., metadata).
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260
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261 It can update or replace read-group information (i.e., information about the samples in the file), add or replace comment lines, and rename reference sequences declared in the header.
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262
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263 The tool ensures that the resulting BAM file is valid and can be further processed by other MiModD tools and standard software like samtools. It aborts with an error message if a valid BAM file cannot be generated with the user-specified settings.
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264
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265 The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool.
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266
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267 @HELP_FOOTER@
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268 ]]></help>
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269 <expand macro="citations" />
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270 </tool>