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1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
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2 <description>merge together several Cufflinks assemblies</description>
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3 <expand macro="requirements" />
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4 <expand macro="stdio" />
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5 <macros>
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6 <import>cuff_macros.xml</import>
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7 </macros>
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8 <command interpreter="python">
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9 cuffmerge_wrapper.py
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10 --num-threads="\${GALAXY_SLOTS:-4}"
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11
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12 ## Use annotation reference?
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13 #if $annotation.use_ref_annotation == "Yes":
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14 -g "${annotation.reference_annotation}"
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15 #end if
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16
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17 ## Use sequence data?
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18 #if $seq_data.use_seq_data == "Yes":
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19 -s
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20 #if $seq_data.seq_source.index_source == "history":
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21 --ref_file="${seq_data.seq_source.ref_file}"
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22 #else:
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23 --index="${seq_data.seq_source.index.fields.path}"
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24 #end if
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25 #end if
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26
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27 --min-isoform-fraction="${min_isoform_fraction}"
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28
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29 ## Outputs.
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30 --merged-transcripts="${merged_transcripts}"
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31
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32 @CUFFLINKS_GTF_INPUTS@
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33 </command>
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34 <inputs>
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35 <expand macro="cufflinks_gtf_inputs" />
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36 <conditional name="annotation">
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37 <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
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38 <option value="No">No</option>
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39 <option value="Yes">Yes</option>
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40 </param>
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41 <when value="Yes">
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42 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/>
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43 </when>
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44 <when value="No">
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45 </when>
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46 </conditional>
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47 <conditional name="seq_data">
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48 <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">
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49 <option value="No">No</option>
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50 <option value="Yes">Yes</option>
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51 </param>
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52 <when value="No"></when>
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53 <when value="Yes">
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54 <conditional name="seq_source">
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55 <param name="index_source" type="select" label="Choose the source for the reference list">
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56 <option value="cached">Locally cached</option>
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57 <option value="history">History</option>
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58 </param>
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59 <when value="cached">
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60 <param name="index" type="select" label="Using reference genome">
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61 <options from_data_table="fasta_indexes">
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62 <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
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63 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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64 </options>
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65 </param>
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66 </when>
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67 <when value="history">
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68 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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69 </when>
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70 </conditional>
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71 </when>
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72 </conditional>
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73 <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" />
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74 </inputs>
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75
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76 <outputs>
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77 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/>
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78 </outputs>
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79
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80 <tests>
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81 <!--
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82 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf
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83 -->
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84 <test>
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85 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/>
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86 <param name="use_ref_annotation" value="Yes"/>
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87 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
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88 <param name="min_isoform_fraction" value="0.08" />
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89 <param name="use_seq_data" value="No"/>
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90 <!-- oId assignment differ/are non-deterministic -->
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91 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/>
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92 </test>
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93 </tests>
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94
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95 <help>
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96 **Cuffmerge Overview**
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97
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98 Cuffmerge is part of Cufflinks_. 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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99
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100 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
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101
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102 ------
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103
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104 **Know what you are doing**
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105
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106 .. class:: warningmark
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107
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108 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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109
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110 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge
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111
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112 ------
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113
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114 **Input format**
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115
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116 Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_)
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117
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118 .. _Ensembl: http://www.ensembl.org
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119
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120 ------
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121
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122 **Outputs**
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123
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124 Cuffmerge produces the following output files:
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125
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126 Merged transcripts file:
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127
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128 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.
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129 </help>
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130 <citations>
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131 <citation type="doi">10.1038/nbt.1621</citation>
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132 </citations>
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133 </tool>
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