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annotate cuffdata_datasets.xml @ 15:2d7eee38ab5b

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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 13:28:44 -0600
parents 9d25b0fd882b
children
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9d25b0fd882b Add cuffdatadb datatype (cummeRbund SQLite DB) to cuffdata.py
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1 <tool id="cuffdata_datasets" name="Cuffdata datasets" version="0.0.6">
1
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2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
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3 <description>history datasets from Cuffdiff output</description>
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4 <requirements>
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5 <requirement type="package">cufflinks</requirement>
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6 </requirements>
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7 <command>
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8 #set sel_outputs = $output_sel.__str__.split(',')
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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9 #if 'run_info' in $sel_outputs:
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10 cat ${cuffdata.extra_files_path}/run.info > $run_info;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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11 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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12 #if 'read_groups_info' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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13 cat ${cuffdata.extra_files_path}/read_groups.info > $read_groups_info;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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14 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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15
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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16 #if 'splicing_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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17 cat ${cuffdata.extra_files_path}/splicing.diff > $splicing_diff;
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18 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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19 #if 'promoters_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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20 cat ${cuffdata.extra_files_path}/promoters.diff > $promoters_diff;
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21 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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22
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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23 #if 'cds_diff' in $sel_outputs:
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24 cat ${cuffdata.extra_files_path}/cds.diff > $cds_diff;
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25 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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26 #if 'cds_exp_diff' in $sel_outputs:
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27 cat ${cuffdata.extra_files_path}/cds_exp.diff > $cds_exp_diff;
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28 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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29 #if 'cds_fpkm_tracking' in $sel_outputs:
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30 cat ${cuffdata.extra_files_path}/cds.fpkm_tracking > $cds_fpkm_tracking;
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31 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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32 #if 'cds_count_tracking' in $sel_outputs:
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33 cat ${cuffdata.extra_files_path}/cds.count_tracking > $cds_count_tracking;
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34 #end if
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35 #if 'cds_read_group_tracking' in $sel_outputs:
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36 cat ${cuffdata.extra_files_path}/cds.read_group_tracking > $cds_read_group_tracking;
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37 #end if
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38
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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39 #if 'tss_groups_exp_diff' in $sel_outputs:
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40 cat ${cuffdata.extra_files_path}/tss_groups_exp.diff > $tss_groups_exp_diff;
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41 #end if
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42 #if 'tss_groups_fpkm_tracking' in $sel_outputs:
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43 cat ${cuffdata.extra_files_path}/tss_groups.fpkm_tracking > $tss_groups_fpkm_tracking;
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44 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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45 #if 'tss_groups_count_tracking' in $sel_outputs:
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46 cat ${cuffdata.extra_files_path}/tss_groups.count_tracking > $tss_groups_count_tracking;
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47 #end if
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48 #if 'tss_groups_read_group_tracking' in $sel_outputs:
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49 cat ${cuffdata.extra_files_path}/tss_groups.read_group_tracking > $tss_groups_read_group_tracking;
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50 #end if
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51
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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52 #if 'genes_exp_diff' in $sel_outputs:
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53 cat ${cuffdata.extra_files_path}/genes_exp.diff > $genes_exp_diff;
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54 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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55 #if 'genes_fpkm_tracking' in $sel_outputs:
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56 cat ${cuffdata.extra_files_path}/genes.fpkm_tracking > $genes_fpkm_tracking;
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57 #end if
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58 #if 'genes_count_tracking' in $sel_outputs:
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59 cat ${cuffdata.extra_files_path}/genes.count_tracking > $genes_count_tracking;
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60 #end if
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61 #if 'genes_read_group_tracking' in $sel_outputs:
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62 cat ${cuffdata.extra_files_path}/genes.read_group_tracking > $genes_read_group_tracking;
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63 #end if
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64
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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65 #if 'isoforms_exp_diff' in $sel_outputs:
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66 cat ${cuffdata.extra_files_path}/isoforms_exp.diff > $isoforms_exp_diff;
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67 #end if
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68 #if 'isoforms_fpkm_tracking' in $sel_outputs:
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69 cat ${cuffdata.extra_files_path}/isoforms.fpkm_tracking > $isoforms_fpkm_tracking;
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70 #end if
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71 #if 'isoforms_count_tracking' in $sel_outputs:
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72 cat ${cuffdata.extra_files_path}/isoforms.count_tracking > $isoforms_count_tracking;
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73 #end if
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74 #if 'isoforms_read_group_tracking' in $sel_outputs:
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75 cat ${cuffdata.extra_files_path}/isoforms.read_group_tracking > $isoforms_read_group_tracking;
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76 #end if
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77
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78 </command>
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79 <inputs>
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80 <param name="cuffdata" type="data" format="cuffdata" label="Cuffidif cuffdata" help=""/>
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81 <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
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82 <option value="run_info">run.info</option>
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83 <option value="read_groups_info">read_groups.info</option>
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84 <option value="splicing_diff">splicing.diff</option>
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85 <option value="promoters_diff">promoters.diff</option>
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86 <option value="genes_exp_diff">genes_exp.diff</option>
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87 <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
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88 <option value="genes_count_tracking">genes.count_tracking</option>
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89 <option value="genes_read_group_tracking">genes.read_group_tracking</option>
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90 <option value="isoforms_exp_diff">isoforms.exp_diff</option>
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91 <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
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92 <option value="isoforms_count_tracking">isoforms.count_tracking</option>
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93 <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
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94 <option value="cds_diff">cds.diff</option>
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95 <option value="cds_exp_diff">cds_exp.diff</option>
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96 <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
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97 <option value="cds_count_tracking">cds.count_tracking</option>
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98 <option value="cds_read_group_tracking">cds.read_group_tracking</option>
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99 <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
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100 <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
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101 <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
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102 <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
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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="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
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108 <filter>'run_info' in output_sel</filter>
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109 </data>
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110 <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
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111 <filter>'read_groups_info' in output_sel</filter>
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112 </data>
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113 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
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114 <filter>'splicing_diff' in output_sel</filter>
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115 </data>
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116 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
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117 <filter>'promoters_diff' in output_sel</filter>
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118 </data>
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119 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
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120 <filter>'cds_diff' in output_sel</filter>
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121 </data>
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122 <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
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123 <filter>'cds_exp_diff' in output_sel</filter>
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124 </data>
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125 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
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126 <filter>'cds_fpkm_tracking' in output_sel</filter>
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127 </data>
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128 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
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129 <filter>'cds_count_tracking' in output_sel</filter>
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130 </data>
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131 <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
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132 <filter>'cds_read_group_tracking' in output_sel</filter>
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133 </data>
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134 <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
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135 <filter>'tss_groups_exp_diff' in output_sel</filter>
1
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136 </data>
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137 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
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138 <filter>'tss_groups_fpkm_tracking' in output_sel</filter>
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139 </data>
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140 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
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141 <filter>'tss_groups_count_tracking' in output_sel</filter>
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142 </data>
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143 <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
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144 <filter>'tss_groups_read_group_tracking' in output_sel</filter>
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145 </data>
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146 <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
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147 <filter>'isoforms_exp_diff' in output_sel</filter>
1
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148 </data>
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149 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
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150 <filter>'isoforms_fpkm_tracking' in output_sel</filter>
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151 </data>
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152 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
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153 <filter>'isoforms_count_tracking' in output_sel</filter>
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154 </data>
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155 <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
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156 <filter>'isoforms_read_group_tracking' in output_sel</filter>
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157 </data>
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158 <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
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159 <filter>'genes_exp_diff' in output_sel</filter>
1
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160 </data>
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161 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
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162 <filter>'genes_fpkm_tracking' in output_sel</filter>
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163 </data>
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164 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
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165 <filter>'genes_count_tracking' in output_sel</filter>
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166 </data>
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167 <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
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168 <filter>'genes_read_group_tracking' in output_sel</filter>
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169 </data>
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170 </outputs>
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171 <stdio>
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172 <exit_code range="1:" level="fatal" description="Cufflinks Err" />
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173 </stdio>
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174
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175
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176 <tests>
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177 </tests>
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178
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179 <help>
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180 **Cuffdata to history datasets**
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181
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182 Copy Cuffdiff output files from a cuffdata html page to datasets in your history.
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183
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184 Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
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185
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186 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
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187
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188 </help>
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189 </tool>