Mercurial > repos > iuc > tetoolkit_tetranscripts

annotate tetranscript.xml @ 0:2dfbcb88d16a draft

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"planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
author iuc
date Wed, 13 May 2020 12:57:29 -0400
parents
children bf4ee2810759
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0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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1 <?xml version="1.0"?>
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2 <tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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3 <description>annotates reads to genes and transposable elements</description>
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4 <macros>
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5 <token name="@TOOL_VERSION@">2.1.4</token>
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6 <token name="@WRAPPER_VERSION@">galaxy0</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">tetranscripts</requirement>
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10 </requirements>
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11 <version_command>TEtranscripts --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ## initialize
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14 ## file extension is required
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15 ln -s '$GTF' 'gene_annotation.gtf' &&
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16 ln -s '$TE' 'transposable_annotation.gtf' &&
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17
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18 ## run
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19 TEtranscripts
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20 ## required
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21 -t
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22 #for $s in $sample_rep
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23 '${s.t}'
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24 #end for
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25 -c
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26 #for $s in $sample_rep
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27 '${s.c}'
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28 #end for
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29 --GTF 'gene_annotation.gtf'
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30 --TE 'transposable_annotation.gtf'
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31 ## optional
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32 --stranded '$io.stranded'
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33 $io.sortByPos
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34 --project 'result'
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35 --mode '$ap.mode'
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36 --minread $ap.minread
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37 #if $ap.fragmentLength
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38 --fragmentLength $ap.fragmentLength
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39 #end if
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40 --iteration $ap.iteration
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41 --padj $ap.padj
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42 --foldchange $ap.foldchange
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43 #if 'log' in $ap.out
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44 --verbose 3
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45 |& tee log.txt
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46 #end if
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47 ]]></command>
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48 <inputs>
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49 <repeat name="sample_rep" min="2" title="Select input data">
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50 <param argument="-t" type="data" format="bam" label="Treatment sample file"/>
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51 <param argument="-c" type="data" format="bam" label="Control sample file"/>
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52 </repeat>
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53 <param argument="--GTF" type="data" format="gtf" label="Select GTF file for gene annotations"/>
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54 <param argument="--TE" type="data" format="gtf" label="Select GTF file for transposable element annotations"/>
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55 <section name="io" title="Input options">
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56 <param argument="--stranded" type="select" label="Select library type">
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57 <option value="no">Library is unstranded (no)</option>
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58 <option value="forward">Second-strand cDNA library e.g. QIAseq stranded (forward)</option>
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59 <option value="reverse">First-strand cDNA library e.g. Illumina TruSeq stranded (reverse)</option>
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60 </param>
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61 <param argument="--sortByPos" type="boolean" truevalue="--sortByPos" falsevalue="" label="Are input files sorted by chromosome position?"/>
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62 </section>
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63 <section name="ap" title="Advanced parameters">
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64 <param argument="--mode" type="select" label="Set TE counting mode">
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65 <option value="multi">Distribute among all alignments (multi)</option>
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66 <option value="uniq">Unique mappers only (uniq)</option>
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67 </param>
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68 <param argument="--minread" type="integer" value="1" min="0" label="Set read count cutoff"/>
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69 <param argument="--fragmentLength" type="integer" min="0" optional="true" label="Set average length of fragment used for single-end sequencing" help="For paired-end, estimated from the input alignment file. For single-end, ignored by default."/>
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70 <param argument="--iteration" type="integer" value="100" min="0" label="Set maximum number of iterations used to optimize multi-reads assignment"/>
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71 <param argument="--padj" type="float" value="0.05" min="0.0" max="1.0" label="Set FDR cutoff for significance"/>
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72 <param argument="--foldchange" type="float" value="1.0" min="0.0" label="Set fold-change ratio (absolute) cutoff for differential expression"/>
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73 <param name="out" type="select" multiple="true" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied.">
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74 <option value="cnttable" selected="true">cntTable</option>
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75 <option value="deseq2" selected="true">DESeq2.R</option>
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76 <option value="gta" selected="true">Gene TE Analysis</option>
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77 <option value="sgt" selected="true">SigDiff Gene TE</option>
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78 <option value="log">Log</option>
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79 </param>
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80 </section>
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81 </inputs>
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82 <outputs>
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83 <data name="out_cnt" format="tabular" from_work_dir="result.cntTable" label="${tool.name} on ${on_string}: cntTable">
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84 <filter>'cnttable' in ap['out']</filter>
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85 </data>
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86 <data name="out_deseq2" format="txt" from_work_dir="result_DESeq2.R" label="${tool.name} on ${on_string}: DESeq2.R">
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87 <filter>'deseq2' in ap['out']</filter>
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88 </data>
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89 <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log">
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90 <filter>'log' in ap['out']</filter>
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iuc
parents:
diff changeset
91 </data>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
92 <data name="out_gta" format="txt" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
93 <filter>'gta' in ap['out']</filter>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
94 </data>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
95 <data name="out_sgt" format="txt" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
96 <filter>'sgt' in ap['out']</filter>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
97 </data>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
98 </outputs>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
99 <tests>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
100 <!--
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
101 sources for test data:
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
102 https://github.com/mhammell-laboratory/tetoolkit-test-data
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
103 https://github.com/mhammell-laboratory/TEtranscripts/issues/66
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
104 -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
105
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
106 <!-- #1: default -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
107 <test expect_num_outputs="5">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
108 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
109 <param name="t" value="treatment1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
110 <param name="c" value="control1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
111 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
112 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
113 <param name="t" value="treatment2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
114 <param name="c" value="control2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
115 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
116 <param name="GTF" value="gtf.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
117 <param name="TE" value="te.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
118 <section name="ap">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
119 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
120 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
121 <output name="out_cnt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
122 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
123 <has_n_lines n="295"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
124 <!-- depends on sample names -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
125 <has_text_matching expression="gene.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
126 <!-- order changes -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
127 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
128 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
129 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
130 <output name="out_deseq2">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
131 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
132 <has_n_lines n="14"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
133 <has_text_matching expression="data.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
134 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
135 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
136 <output name="out_log">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
137 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
138 <has_text_matching expression="INFO"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
139 <has_text_matching expression=".+Done"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
140 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
141 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
142 <output name="out_gta">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
143 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
144 <has_n_lines n="71"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
145 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
146 <!-- order changes -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
147 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
148 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
149 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
150 <!-- no content, test dataset to small -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
151 <output name="out_sgt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
152 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
153 <has_n_lines n="1"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
154 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
155 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
156 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
157 </test>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
158 <!-- #2 -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
159 <test expect_num_outputs="5">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
160 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
161 <param name="t" value="treatment1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
162 <param name="c" value="control1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
163 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
164 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
165 <param name="t" value="treatment2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
166 <param name="c" value="control2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
167 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
168 <param name="GTF" value="gtf.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
169 <param name="TE" value="te.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
170 <section name="io">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
171 <param name="stranded" value="forward"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
172 <param name="sortByPos" value="true"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
173 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
174 <section name="ap">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
175 <param name="mode" value="uniq"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
176 <param name="minread" value="2"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
177 <param name="fragmentLength" value="10"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
178 <param name="iteration" value="90"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
179 <param name="padj" value="0.06"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
180 <param name="foldchange" value="2.0"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
181 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
182 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
183 <output name="out_cnt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
184 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
185 <has_n_lines n="295"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
186 <!-- depends on sample names -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
187 <has_text_matching expression="gene.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
188 <!-- order changes -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
189 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
190 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
191 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
192 <output name="out_deseq2">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
193 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
194 <has_n_lines n="14"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
195 <has_text_matching expression="data.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
196 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
197 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
198 <output name="out_log">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
199 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
200 <has_text_matching expression="INFO.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
201 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
202 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
203 <output name="out_gta">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
204 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
205 <has_n_lines n="3"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
206 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
207 <!-- order changes -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
208 <has_text_matching expression="DNAREP1.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
209 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
210 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
211 <!-- no content, test dataset to small -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
212 <output name="out_sgt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
213 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
214 <has_n_lines n="1"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
215 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
216 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
217 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
218 </test>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
219 <!-- #3 -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
220 <test expect_num_outputs="5">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
221 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
222 <param name="t" value="treatment1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
223 <param name="c" value="control1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
224 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
225 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
226 <param name="t" value="treatment2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
227 <param name="c" value="control2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
228 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
229 <param name="GTF" value="gtf.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
230 <param name="TE" value="te.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
231 <section name="io">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
232 <param name="stranded" value="reverse"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
233 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
234 <section name="ap">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
235 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
236 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
237 <output name="out_cnt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
238 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
239 <has_n_lines n="295"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
240 <!-- depends on sample names -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
241 <has_text_matching expression="gene.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
242 <!-- order changes -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
243 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
244 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
245 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
246 <output name="out_deseq2">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
247 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
248 <has_n_lines n="14"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
249 <has_text_matching expression="data.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
250 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
251 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
252 <output name="out_log">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
253 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
254 <has_text_matching expression="INFO.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
255 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
256 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
257 <output name="out_gta">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
258 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
259 <has_n_lines n="23"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
260 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
261 <!-- order changes -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
262 <has_text_matching expression="TART.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
263 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
264 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
265 <output name="out_sgt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
266 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
267 <has_n_lines n="2"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
268 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
269 <has_text_matching expression="Gypsy12.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
270 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
271 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
272 </test>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
273 </tests>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
274 <help><![CDATA[
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
275 .. class:: infomark
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
276
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
277 **What it does**
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
278
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
279 TEtranscripts is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments. Currently, most expression analysis software packates are not optimized for handling the complexities involved in quantifying highly repetitive regions of the genome, especially transposable elements (TE), from short sequencing reads. Although transposon elements make up between 20 to 80% of many eukaryotic genomes and contribute significantly to the cellular transcriptome output, the difficulty in quantifying their abundances from high throughput sequencing experiments has led them to be largely ignored in most studies. The TEtranscripts provides a noticeable improvement in the recovery of TE transcripts from RNA-Seq experiments and identification of peaks associated with repetitive regions of the genome.
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
280
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
281 **Input**
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
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282
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283 GTF files for gene annotation can be obtained from `UCSC RefSeq <http://genome.ucsc.edu/cgi-bin/hgTables>`_, Ensembl, `iGenomes <http://support.illumina.com/sequencing/sequencing_software/igenome.html>`_ or other annotation databases. GTF files for TE annotations are customly generated from `UCSC RepeatMasker <http://genome.ucsc.edu/cgi-bin/hgTables>`_ or other annotation database. They contain two custom attributes, class_id and family_id, corresponding to the class (e.g. LINE) and family (e.g. L1) of the corresponding transposable element. A unique ID (e.g. L1Md_Gf_dup1) is also assigned for each TE annotation in the transcript_id attribute.
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284
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285 **Output**
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286
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287 TEtranscripts quantifies both gene and transposable element (TE) transcript abundances from RNA-Seq experiments, utilizing both uniquely and ambiguously mapped short read sequences. It processes the short reads alignments (BAM files) and proportionally assigns read counts to the corresponding gene or TE based on the user-provided annotation files (GTF files). In addition, TEtranscripts combines multiple libraries and perform differential analysis using DESeq2.
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288
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289 .. class:: infomark
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290
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291 **References**
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292
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293 More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `github <https://github.com/mhammell-laboratory/TEtranscripts>`_.
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294 ]]></help>
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295 <citations>
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296 <citation type="doi">10.1093/bioinformatics/btv422</citation>
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297 <citation type="doi">10.1007/978-1-4939-7710-9_11</citation>
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298 </citations>
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299 </tool>