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annotate cuffdiff_wrapper.xml @ 8:b0d11fcbc3ac

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cummerbund add MDS and PCA plots, handle errors from R
author Jim Johnson <jj@umn.edu>
date Thu, 11 Oct 2012 15:14:51 -0500
parents 79c687de829b
children 56bdf6d4ac9c
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5
9d25b0fd882b Add cuffdatadb datatype (cummeRbund SQLite DB) to cuffdata.py
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1 <tool id="cuffdiff" name="Cuffdiff" 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>find significant changes in transcript expression, splicing, and promoter use</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 interpreter="python">
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8 #set sel_outputs = $output_sel.__str__.split(',')
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9 cuffdiff_wrapper.py
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10 --FDR=$fdr
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11 --num-threads="4"
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12 --min-alignment-count=$min_alignment_count
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13
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14 #if 'cuffdata' in $sel_outputs or not $output_sel:
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15 --cuffdatadir=$cuffdata.extra_files_path
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16 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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17 #if 'cummeRbund_db' in $sel_outputs:
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18 --cummeRbund_db=$cummeRbund_db
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19 #end if
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20
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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21 #if 'isoforms_fpkm_tracking' in $sel_outputs:
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22 --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking
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23 #end if
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24 #if 'genes_fpkm_tracking' in $sel_outputs:
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25 --genes_fpkm_tracking_output=$genes_fpkm_tracking
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26 #end if
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27 #if 'cds_fpkm_tracking' in $sel_outputs:
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28 --cds_fpkm_tracking_output=$cds_fpkm_tracking
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29 #end if
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30 #if 'tss_groups_fpkm_tracking' in $sel_outputs:
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31 --tss_groups_fpkm_tracking_output=$tss_groups_fpkm_tracking
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32 #end if
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33 #if 'isoforms_exp_diff' in $sel_outputs:
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34 --isoforms_exp_output=$isoforms_exp_diff
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35 #end if
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36 #if 'genes_exp_diff' in $sel_outputs:
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37 --genes_exp_output=$genes_exp_diff
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38 #end if
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39 #if 'tss_groups_exp_diff' in $sel_outputs:
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40 --tss_groups_exp_output=$tss_groups_exp_diff
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41 #end if
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42 #if 'cds_exp_fpkm_tracking' in $sel_outputs:
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43 --cds_exp_fpkm_tracking_output=$cds_exp_fpkm_tracking
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44 #end if
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45 #if 'splicing_diff' in $sel_outputs:
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46 --splicing_diff_output=$splicing_diff
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47 #end if
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48 #if 'cds_diff' in $sel_outputs:
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49 --cds_diff_output=$cds_diff
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50 #end if
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51 #if 'promoters_diff' in $sel_outputs:
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52 --promoters_diff_output=$promoters_diff
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53 #end if
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54 #if 'cds_read_group_tracking' in $sel_outputs:
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55 --cds_read_group_tracking=$cds_read_group_tracking
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56 #end if
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57 #if 'tss_groups_read_group_tracking' in $sel_outputs:
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58 --tss_groups_read_group_tracking=$tss_groups_read_group_tracking
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59 #end if
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60 #if 'genes_read_group_tracking' in $sel_outputs:
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61 --genes_read_group_tracking=$genes_read_group_tracking
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62 #end if
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63 #if 'isoforms_read_group_tracking' in $sel_outputs:
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64 --isoforms_read_group_tracking=$isoforms_read_group_tracking
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65 #end if
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66
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67 ## Set advanced data parameters?
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68 #if $additional.sAdditional == "Yes":
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69 -m $additional.frag_mean_len
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70 -s $additional.frag_len_std_dev
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71 #end if
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72
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73 ## Normalization?
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74 #if str($do_normalization) == "Yes":
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75 -N
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76 #end if
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77
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78 ## Multi-read correct?
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79 #if str($multiread_correct) == "Yes":
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80 -u
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81 #end if
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82
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83 ## Bias correction?
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84 #if $bias_correction.do_bias_correction == "Yes":
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85 -b
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86 #if $bias_correction.seq_source.index_source == "history":
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87 --ref_file=$bias_correction.seq_source.ref_file
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88 #else:
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89 --ref_file="None"
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90 #end if
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91 --dbkey=${gtf_input.metadata.dbkey}
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92 --index_dir=${GALAXY_DATA_INDEX_DIR}
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93 #end if
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94
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95 ## Inputs.
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96 --inputA=$gtf_input
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97 #if $group_analysis.do_groups == "No":
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98 --input1=$aligned_reads1
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99 --input2=$aligned_reads2
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100 #else:
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101 ## Replicates.
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102 --labels
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103 #for $group in $group_analysis.groups
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104 ${group.group}
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105 #end for
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106 --files
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107 #for $group in $group_analysis.groups
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108 #for $file in $group.files:
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109 ${file.file}
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110 #end for
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111 ,
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112 #end for
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113 #end if
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114
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115 </command>
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116 <inputs>
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117 <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/>
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118 <conditional name="group_analysis">
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119 <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group.">
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120 <option value="No">No</option>
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121 <option value="Yes">Yes</option>
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122 </param>
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123 <when value="Yes">
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124 <repeat name="groups" title="Group">
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125 <param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/>
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126 <repeat name="files" title="Replicate">
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127 <param name="file" label="Add file" type="data" format="sam,bam"/>
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diff changeset
128 </repeat>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
129 </repeat>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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diff changeset
130 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
131 <when value="No">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
132 <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
133 <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
134 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
135 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
136
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
137 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
138
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
139 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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diff changeset
140
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
141 <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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142 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
143 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
144 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
145
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
146 <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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147 <option value="No" selected="true">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
148 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
149 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
150
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
151 <conditional name="bias_correction">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
152 <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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153 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
154 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
155 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
156 <when value="Yes">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
157 <conditional name="seq_source">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
158 <param name="index_source" type="select" label="Reference sequence data">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
159 <option value="cached">Locally cached</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
160 <option value="history">History</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
161 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
162 <when value="cached"></when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
163 <when value="history">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
164 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
165 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
166 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
167 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 <when value="No"></when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
169 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
171 <conditional name="additional">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
172 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
173 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
174 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
175 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
176 <when value="No"></when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
177 <when value="Yes">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
178 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
180 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
181 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
182
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
183 <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
184 <option value="cuffdata">cuffdata - html page with links to cuffdiff outputs</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
185 <option value="cummeRbund_db">cummeRbund database</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
186 <option value="run_info">run.info</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
187 <option value="read_groups_info">read_groups.info</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 <option value="splicing_diff">splicing.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
189 <option value="promoters_diff">promoters.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
190 <option value="genes_exp_diff">genes_exp.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
191 <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
192 <option value="genes_count_tracking">genes.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
193 <option value="genes_read_group_tracking">genes.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
194 <option value="isoforms_exp_diff">isoforms.exp_diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
195 <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
196 <option value="isoforms_count_tracking">isoforms.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
197 <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
198 <option value="cds_diff">cds.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
199 <option value="cds_exp_diff">cds_exp.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
200 <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
201 <option value="cds_count_tracking">cds.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
202 <option value="cds_read_group_tracking">cds.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
204 <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
205 <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
206 <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
207 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
208
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
209 </inputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
210
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
211 <outputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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parents:
diff changeset
212 <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
213 <filter>output_sel and 'run_info' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
214 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
215 <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
216 <filter>output_sel and 'read_groups_info' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
217 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
218 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
219 <filter>output_sel and 'splicing_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
220 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
221 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
222 <filter>output_sel and 'promoters_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
223 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
224 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
225 <filter>output_sel and 'cds_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
226 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
227 <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
228 <filter>output_sel and 'cds_exp_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
229 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
230 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 <filter>output_sel and 'cds_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
233 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
234 <filter>output_sel and 'cds_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
235 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
236 <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
237 <filter>output_sel and 'cds_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
238 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
240 <filter>output_sel and 'tss_groups_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
241 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
242 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
243 <filter>output_sel and 'tss_groups_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
244 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
245 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
246 <filter>output_sel and 'tss_groups_count_tracking' in output_sel</filter>
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247 </data>
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248 <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
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249 <filter>output_sel and 'tss_groups_read_group_tracking' in output_sel</filter>
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250 </data>
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251 <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
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252 <filter>output_sel and 'isoforms_exp_diff' in output_sel</filter>
1
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253 </data>
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254 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
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255 <filter>output_sel and 'isoforms_fpkm_tracking' in output_sel</filter>
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256 </data>
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257 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
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258 <filter>output_sel and 'isoforms_count_tracking' in output_sel</filter>
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259 </data>
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260 <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
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261 <filter>output_sel and 'isoforms_read_group_tracking' in output_sel</filter>
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262 </data>
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263 <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
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264 <filter>output_sel and 'genes_exp_diff' in output_sel</filter>
1
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265 </data>
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266 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
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267 <filter>output_sel and 'genes_fpkm_tracking' in output_sel</filter>
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268 </data>
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269 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
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270 <filter>output_sel and 'genes_count_tracking' in output_sel</filter>
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271 </data>
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272 <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
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273 <filter>output_sel and 'genes_read_group_tracking' in output_sel</filter>
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274 </data>
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275 <data format="cuffdata" name="cuffdata" label="${tool.name} on ${on_string}: cuffdata" >
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276 <filter>not output_sel or output_sel and 'cuffdata' in output_sel</filter>
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277 </data>
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278 <data format="cuffdatadb" name="cummeRbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
1
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279 <filter>output_sel and 'cummeRbund_db' in output_sel</filter>
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280 </data>
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281 </outputs>
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282 <stdio>
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283 <exit_code range="1:" level="fatal" description="Cufflinks Err" />
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284 </stdio>
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285
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286
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287 <tests>
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288 <test>
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289 <!--
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290 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
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291 -->
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292 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
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293 <param name="do_groups" value="No" />
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294 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
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295 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
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296 <!-- Defaults. -->
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297 <param name="fdr" value="0.05" />
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298 <param name="min_alignment_count" value="0" />
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299 <param name="do_bias_correction" value="No" />
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300 <param name="do_normalization" value="No" />
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301 <param name="multiread_correct" value="No"/>
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302 <param name="sAdditional" value="No"/>
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303 <!--
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304 Line diffs are needed because cuffdiff does not produce deterministic output.
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305 TODO: can we find datasets that lead to deterministic behavior?
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306 -->
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307 <output name="splicing_diff" file="cuffdiff_out9.txt"/>
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308 <output name="promoters_diff" file="cuffdiff_out10.txt"/>
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309 <output name="cds_diff" file="cuffdiff_out11.txt"/>
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310 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
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311 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
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312 <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
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313 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
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314 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
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315 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
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316 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
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317 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
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318 </test>
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319 </tests>
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320
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321 <help>
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322 **Cuffdiff Overview**
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323
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324 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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325
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326 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
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327
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328 ------
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329
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330 **Know what you are doing**
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331
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332 .. class:: warningmark
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333
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334 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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335
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336 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
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337
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338 ------
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339
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340 **Input format**
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341
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342 Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
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343
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344 ------
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345
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346 **Outputs**
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347
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348 Cuffdiff produces many output files:
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349
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350 1. Transcript FPKM expression tracking.
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351 2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id
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352 3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id
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353 4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id
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354 5. Transcript differential FPKM.
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355 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id
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356 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id
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357 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id
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358 9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file.
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359 10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here.
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360 11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here.
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361
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362 -------
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363
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364 **Settings**
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365
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366 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
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367
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368 ------
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369
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370 **Cuffdiff parameter list**
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371
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372 This is a list of implemented Cuffdiff options::
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373
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374 -m INT Average fragement length; default 200
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375 -s INT Fragment legnth standard deviation; default 80
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376 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).
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377 --FDR FLOAT The allowed false discovery rate. The default is 0.05.
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378 --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000
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379 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
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380 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
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381
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382 </help>
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383 </tool>