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annotate tetranscript.xml @ 4:8e96d712a2bd draft default tip

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planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 3de50462b3bbe717953c65a1c00935999327a4f0
author iuc
date Thu, 03 Nov 2022 18:17:35 +0000
parents 313414e9abcf
children
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1 <?xml version="1.0"?>
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2 <tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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@">2.2.3</token>
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6 <token name="@VERSION_SUFFIX@">0</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 $oo.out
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44 --verbose 3
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45 |& tee '$out_log'
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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 file for gene annotations"/>
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54 <param argument="--TE" type="data" format ="gtf" label="Select file for transposable element annotations"/>
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55 <section name="io" title="Input options" expanded="true">
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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 </section>
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74 <section name="oo" title="Output options">
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75 <param name="out" type="select" multiple="true" optional="false" 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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76 <option value="cnttable" selected="true">cntTable</option>
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77 <option value="deseq2">DESeq2.R</option>
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78 <option value="gta" selected="true">Gene TE Analysis</option>
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79 <option value="log">Log</option>
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80 <option value="sgt" selected="true">SigDiff Gene TE</option>
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81 </param>
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82 </section>
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83 </inputs>
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84 <outputs>
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85 <data name="out_cnt" format="tabular" from_work_dir="result.cntTable" label="${tool.name} on ${on_string}: cntTable">
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86 <filter>'cnttable' in oo['out']</filter>
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87 </data>
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88 <data name="out_deseq2" format="txt" from_work_dir="result_DESeq2.R" label="${tool.name} on ${on_string}: DESeq2.R">
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89 <filter>'deseq2' in oo['out']</filter>
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90 </data>
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91 <data name="out_gta" format="tabular" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis">
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parents: 1
diff changeset
92 <filter>'gta' in oo['out']</filter>
0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
93 </data>
3
313414e9abcf "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 3e9f9ddaec68db309cfc75d6201236746b41a95e"
iuc
parents: 2
diff changeset
94 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
2
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
95 <filter>'log' in oo['out']</filter>
0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
96 </data>
2
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
97 <data name="out_sgt" format="tabular" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE">
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
98 <filter>'sgt' in oo['out']</filter>
0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
99 </data>
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parents:
diff changeset
100 </outputs>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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parents:
diff changeset
101 <tests>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
102 <!--
1
bf4ee2810759 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit de0508a070ac11901c5c4cb9caffea85f0c889fb"
iuc
parents: 0
diff changeset
103 test data sources:
0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
104 https://github.com/mhammell-laboratory/tetoolkit-test-data
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iuc
parents:
diff changeset
105 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
106 -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
107
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
108 <!-- #1: default -->
2
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iuc
parents: 1
diff changeset
109 <test expect_num_outputs="3">
0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
110 <repeat name="sample_rep">
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iuc
parents:
diff changeset
111 <param name="t" value="treatment1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
112 <param name="c" value="control1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
113 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
114 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
115 <param name="t" value="treatment2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
116 <param name="c" value="control2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
117 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
118 <param name="GTF" value="gtf.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
119 <param name="TE" value="te.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
120 <output name="out_cnt">
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iuc
parents:
diff changeset
121 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
122 <has_n_lines n="295"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
123 <has_text_matching expression="gene.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
124 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
125 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
126 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
127 <output name="out_gta">
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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 <has_n_lines n="71"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
130 <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
131 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
132 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
133 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
134 <output name="out_sgt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
135 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
136 <has_n_lines n="1"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
137 <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
138 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
139 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
140 </test>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
141 <!-- #2 -->
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
142 <test expect_num_outputs="5">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
143 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
144 <param name="t" value="treatment1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
145 <param name="c" value="control1.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
146 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
147 <repeat name="sample_rep">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
148 <param name="t" value="treatment2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
149 <param name="c" value="control2.bam"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
150 </repeat>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
151 <param name="GTF" value="gtf.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
152 <param name="TE" value="te.gtf"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
153 <section name="io">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
154 <param name="stranded" value="forward"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
155 <param name="sortByPos" value="true"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
156 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
157 <section name="ap">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
158 <param name="mode" value="uniq"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
159 <param name="minread" value="2"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
160 <param name="fragmentLength" value="10"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
161 <param name="iteration" value="90"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
162 <param name="padj" value="0.06"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
163 <param name="foldchange" value="2.0"/>
2
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
164 </section>
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
165 <section name="oo">
0
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
166 <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
167 </section>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
168 <output name="out_cnt">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
169 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
170 <has_n_lines n="295"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
171 <has_text_matching expression="gene.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
172 <has_text_matching expression="TIRANT.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
173 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
174 </output>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
175 <output name="out_deseq2">
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
176 <assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
177 <has_n_lines n="14"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
178 <has_text_matching expression="data.+"/>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
179 </assert_contents>
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
iuc
parents:
diff changeset
180 </output>
2
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
181 <output name="out_gta">
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
182 <assert_contents>
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
183 <has_n_lines n="3"/>
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
184 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
185 <has_text_matching expression="DNAREP1.+"/>
bbeab8445490 "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
iuc
parents: 1
diff changeset
186 </assert_contents>
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187 </output>
0
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188 <output name="out_log">
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189 <assert_contents>
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190 <has_text_matching expression="INFO.+"/>
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191 </assert_contents>
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192 </output>
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193 <output name="out_sgt">
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194 <assert_contents>
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195 <has_n_lines n="1"/>
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196 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
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197 </assert_contents>
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198 </output>
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199 </test>
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200 <!-- #3 -->
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201 <test expect_num_outputs="5">
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202 <repeat name="sample_rep">
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203 <param name="t" value="treatment1.bam"/>
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204 <param name="c" value="control1.bam"/>
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205 </repeat>
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206 <repeat name="sample_rep">
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207 <param name="t" value="treatment2.bam"/>
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208 <param name="c" value="control2.bam"/>
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209 </repeat>
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210 <param name="GTF" value="gtf.gtf"/>
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211 <param name="TE" value="te.gtf"/>
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212 <section name="io">
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213 <param name="stranded" value="reverse"/>
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214 </section>
2
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215 <section name="oo">
0
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216 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
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217 </section>
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218 <output name="out_cnt">
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219 <assert_contents>
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220 <has_n_lines n="295"/>
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221 <has_text_matching expression="gene.+"/>
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222 <has_text_matching expression="TIRANT.+"/>
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223 </assert_contents>
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224 </output>
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225 <output name="out_deseq2">
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226 <assert_contents>
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227 <has_n_lines n="14"/>
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228 <has_text_matching expression="data.+"/>
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229 </assert_contents>
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230 </output>
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231 <output name="out_gta">
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232 <assert_contents>
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233 <has_n_lines n="23"/>
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234 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
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235 <has_text_matching expression="TART.+"/>
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236 </assert_contents>
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237 </output>
2
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238 <output name="out_log">
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239 <assert_contents>
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240 <has_text_matching expression="INFO.+"/>
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241 </assert_contents>
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242 </output>
0
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243 <output name="out_sgt">
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244 <assert_contents>
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245 <has_n_lines n="2"/>
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246 <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
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247 <has_text_matching expression="Gypsy12.+"/>
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248 </assert_contents>
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249 </output>
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250 </test>
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251 </tests>
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252 <help><![CDATA[
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253 .. class:: infomark
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254
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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255 **What it does**
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256
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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257 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.
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258
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259 **Input**
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260
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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261 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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262
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263 **Output**
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264
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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265 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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266
2dfbcb88d16a "planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
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267 .. class:: infomark
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268
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269 **References**
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270
2
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271 More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `GitHub <https://github.com/mhammell-laboratory/TEtranscripts>`_.
0
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272 ]]></help>
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273 <citations>
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274 <citation type="doi">10.1093/bioinformatics/btv422</citation>
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275 <citation type="doi">10.1007/978-1-4939-7710-9_11</citation>
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276 </citations>
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277 </tool>