Mercurial > repos > iuc > deseq2
annotate deseq2.xml @ 43:621ddf5967d2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
author | iuc |
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date | Tue, 18 Jul 2023 14:58:28 +0000 |
parents | 6ef2cba4e35a |
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rev | line source |
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43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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changeset
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1 <tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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2 <description>Determines differentially expressed features from count tables</description> |
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f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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3 <macros> |
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621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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4 <import>macros.xml</import> |
34
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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5 </macros> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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changeset
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6 <expand macro='edam_ontology'/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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7 <expand macro='xrefs'/> |
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b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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8 <expand macro='requirements'/> |
6
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
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9 <stdio> |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
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10 <regex match="Execution halted" |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
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11 source="both" |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
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12 level="fatal" |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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13 description="Execution halted."/> |
6
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
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14 <regex match="Error in" |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
parents:
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15 source="both" |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
parents:
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16 level="fatal" |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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17 description="An undefined error occurred, please check your input carefully and contact your administrator."/> |
6
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
parents:
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changeset
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18 <regex match="Fatal error" |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
parents:
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diff
changeset
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19 source="both" |
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
parents:
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changeset
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20 level="fatal" |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
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21 description="An undefined error occurred, please check your input carefully and contact your administrator."/> |
6
982bd8bfa44c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
iuc
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22 </stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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23 <version_command><![CDATA[ |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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24 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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25 ]]></version_command> |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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26 <command><![CDATA[ |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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27 #if $tximport.tximport_selector == 'tximport': |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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28 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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29 ln -s '$tximport.mapping_format.gtf_file' mapping.gff && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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30 #else: |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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31 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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32 #end if |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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33 #end if |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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34 |
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cf2c5e8ea088
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
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35 ## This is needed for Pulsar to transfer the file |
cf2c5e8ea088
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
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36 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null && |
cf2c5e8ea088
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
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37 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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38 #import json |
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1a34aec44d60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
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39 #import os |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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40 Rscript '${__tool_directory__}/deseq2.R' |
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4f497a8a72e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3
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41 --cores \${GALAXY_SLOTS:-1} |
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d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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42 -o '$deseq_out' |
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b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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43 #if 'pdf' in $output_options.output_selector: |
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d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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44 -p '$plots' |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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45 #end if |
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b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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46 -A $output_options.alpha_ma |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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47 #if 'normCounts' in $output_options.output_selector: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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48 -n '$counts_out' |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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49 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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50 #if 'sizefactors' in $output_options.output_selector: |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
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51 -F '$sizefactors_out' |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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52 #end if |
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b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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53 #if 'normRLog' in $output_options.output_selector: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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54 -r '$rlog_out' |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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55 #end if |
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b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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56 #if 'normVST' in $output_options.output_selector: |
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3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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57 -v '$vst_out' |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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58 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
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59 #set $filename_to_element_identifiers = {} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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60 #set $temp_factor_names = list() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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61 #for $factor in $select_data.rep_factorName: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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62 #set $temp_factor = list() |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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63 #for $level in $factor.rep_factorLevel: |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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64 #set $count_files = list() |
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f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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65 #if $select_data.how == 'group_tags': |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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66 #for $group in $level.groups.value: |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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67 #for $file in $select_data.countsFile.get_datasets_for_group($group): |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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68 $count_files.append(str($file)) |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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69 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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70 #end for |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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71 #end for |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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72 #else: |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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73 #for $file in $level.countsFile: |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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74 $count_files.append(str($file)) |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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75 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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76 #end for |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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77 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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78 $temp_factor.append( {str($level.factorLevel): $count_files} ) |
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79 #end for |
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80 $temp_factor.reverse() |
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81 $temp_factor_names.append([str($factor.factorName), $temp_factor]) |
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82 #end for |
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83 |
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84 $header |
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85 |
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86 -f '#echo json.dumps(temp_factor_names)#' |
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87 -l '#echo json.dumps(filename_to_element_identifiers)#' |
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88 #if $advanced_options.esf_cond.esf: |
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89 #if $advanced_options.esf_cond.esf == "user": |
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90 -e $advanced_options.esf_cond.size_factor_input |
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91 #else: |
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92 -e $advanced_options.esf_cond.esf |
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93 #end if |
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94 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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95 -t $advanced_options.fit_type |
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96 #if $batch_factors: |
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97 --batch_factors '$batch_factors' |
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98 #end if |
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99 #if $advanced_options.prefilter_conditional.prefilter: |
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100 $advanced_options.prefilter_conditional.prefilter |
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101 -V $advanced_options.prefilter_conditional.prefilter_value |
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102 #end if |
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103 |
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104 $advanced_options.outlier_replace_off |
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105 $advanced_options.outlier_filter_off |
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106 $advanced_options.auto_mean_filter_off |
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107 $advanced_options.use_beta_priors |
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108 |
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109 #if 'many_contrasts' in $output_options.output_selector |
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110 -m |
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111 #end if |
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112 #if $tximport.tximport_selector == 'tximport': |
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113 -i |
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114 -y $tximport.txtype |
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115 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
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116 -x mapping.gff |
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117 #else: |
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118 -x mapping.txt |
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119 #end if |
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120 #end if |
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121 ]]></command> |
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122 <inputs> |
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123 <conditional name="select_data"> |
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124 <param name="how" type="select"> |
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125 <option value="datasets_per_level">Select datasets per level</option> |
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126 <option value="group_tags">Select group tags corresponding to levels</option> |
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127 </param> |
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128 <when value="group_tags"> |
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129 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/> |
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130 <expand macro="factor_repeat"> |
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131 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/> |
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132 </expand> |
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133 </when> |
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134 <when value="datasets_per_level"> |
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135 <expand macro="factor_repeat"> |
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136 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> |
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137 </expand> |
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138 </when> |
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139 </conditional> |
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140 |
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141 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/> |
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142 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes"/> |
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143 |
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144 <conditional name="tximport"> |
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145 <param name="tximport_selector" type="select" label="Choice of Input data"> |
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146 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> |
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147 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option> |
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148 </param> |
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149 <when value="tximport"> |
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150 <param name="txtype" type="select" label="Program used to generate TPMs"> |
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151 <option value="kallisto">kallisto</option> |
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152 <option value="sailfish">Sailfish</option> |
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153 <option value="salmon">Salmon</option> |
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154 </param> |
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155 <conditional name="mapping_format"> |
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156 <param name="mapping_format_selector" type="select" label="Gene mapping format"> |
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157 <option value="gtf" selected="True">GTF/GFF3</option> |
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158 <option value="tabular">Transcript-ID to Gene-ID mapping file</option> |
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159 </param> |
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160 <when value="gtf"> |
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161 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/> |
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162 </when> |
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163 <when value="tabular"> |
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164 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/> |
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165 </when> |
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166 </conditional> |
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167 </when> |
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168 <when value="count"/> |
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169 </conditional> |
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170 <section name="advanced_options" title="Advanced options"> |
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171 <conditional name="esf_cond"> |
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172 <param name="esf" type="select" label="Method for estimateSizeFactors" |
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173 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq. |
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174 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples. |
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175 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem |
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176 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with |
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177 some zeros, by calculating a modified geometric mean by taking the n-th root of the product of the non-zero counts. This evolved out of |
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178 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion |
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179 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model."> |
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180 <option value="" selected="true">No Selection (use default)</option> |
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181 <option value="ratio">ratio</option> |
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182 <option value="poscounts">poscounts</option> |
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183 <option value="iterate">iterate</option> |
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184 <option value="user">User-provided</option> |
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185 </param> |
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186 <when value=""/> |
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187 <when value="ratio"/> |
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188 <when value="poscounts"/> |
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189 <when value="iterate"/> |
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190 <when value="user"> |
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191 <param name="size_factor_input" type="data" format="tabular" label="File with custom size factors" help="The input must be a 2-column file: col1 should have the input file names. Col2 should contain your custom size factors."/> |
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192 </when> |
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193 </conditional> |
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194 <param name="fit_type" type="select" label="Fit type"> |
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195 <option value="1" selected="true">parametric</option> |
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196 <option value="2">local</option> |
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197 <option value="3">mean</option> |
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198 </param> |
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199 <param name="outlier_replace_off" type="boolean" truevalue="-a" falsevalue="" checked="false" |
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200 label="Turn off outliers replacement (only affects with >6 replicates)" |
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201 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace |
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202 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor |
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203 or normalization factor for that sample"/> |
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204 <param name="outlier_filter_off" type="boolean" truevalue="-b" falsevalue="" checked="false" |
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205 label="Turn off outliers filtering (only affects with >2 replicates)" |
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206 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically |
43
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207 filter genes which contain a Cook’s distance above a cutoff"/> |
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208 <param name="auto_mean_filter_off" type="boolean" truevalue="-c" falsevalue="" checked="false" |
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209 label="Turn off independent filtering" |
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210 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic"/> |
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211 <conditional name="prefilter_conditional"> |
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212 <param name="prefilter" type="select" label="Perform pre-filtering" help="While it is not necessary to pre-filter |
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213 low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful: |
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214 by removing rows in which there are very few reads, we reduce the required memory, and we increase the speed. |
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215 It can also improve visualizations, as features with no information for differential expression are not plotted."> |
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216 <option value="-P">Enabled</option> |
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217 <option value="" selected="true">Disabled</option> |
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218 </param> |
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219 <when value="-P"> |
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220 <param name="prefilter_value" type="integer" min="0" value="10" label="Pre-filter value" help="Keep only rows that have at least N reads total."/> |
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221 </when> |
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222 <when value=""/> |
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223 </conditional> |
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224 <param name="use_beta_priors" type="boolean" truevalue="-d" falsevalue="" checked="false" |
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225 label="Use beta priors" |
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226 help="Whether or not to put a zero-mean normal prior on the non-intercept coefficients"/> |
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227 </section> |
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228 <section name="output_options" title="Output options"> |
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229 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector"> |
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230 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option> |
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231 <option value="sizefactors">Output sample size factors</option> |
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232 <option value="normCounts">Output normalised counts</option> |
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233 <option value="normVST">Output VST normalized table</option> |
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234 <option value="normRLog">Output rLog normalized table</option> |
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235 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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236 </param> |
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237 <param name="alpha_ma" type="float" min="0" max="0.5" value="0.1" label="Alpha value for MA-plot" help="Default value is 0.1. This option is only meaninful when plots are generated"/> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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238 </section> |
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239 </inputs> |
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240 <outputs> |
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241 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}"> |
39
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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242 <filter>'many_contrasts' not in output_options['output_selector']</filter> |
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243 <actions> |
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244 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj"/> |
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245 </actions> |
0
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246 </data> |
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247 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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248 <filter>output_options['output_selector'] and 'many_contrasts' in output_options['output_selector']</filter> |
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d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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249 <discover_datasets pattern="(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> |
0
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250 </collection> |
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251 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> |
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b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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252 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter> |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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253 </data> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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254 <data name="sizefactors_out" format="tabular" label="Size Factors on ${on_string}"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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255 <filter>output_options['output_selector'] and 'sizefactors' in output_options['output_selector']</filter> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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256 </data> |
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257 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}"> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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258 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter> |
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259 </data> |
31
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260 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}"> |
39
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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261 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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262 </data> |
31
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263 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}"> |
39
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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264 <filter>output_options['output_selector'] and 'normVST' in output_options['output_selector']</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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265 </data> |
0
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266 </outputs> |
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267 <tests> |
27
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268 <!--Ensure counts files with header works --> |
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269 <test expect_num_outputs="4"> |
0
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270 <repeat name="rep_factorName"> |
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271 <param name="factorName" value="Treatment"/> |
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272 <repeat name="rep_factorLevel"> |
5b1ce9db498e
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273 <param name="factorLevel" value="Treated"/> |
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274 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
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275 </repeat> |
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276 <repeat name="rep_factorLevel"> |
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277 <param name="factorLevel" value="Untreated"/> |
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278 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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279 </repeat> |
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280 </repeat> |
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281 <section name="advanced_options"> |
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282 <param name="use_beta_priors" value="1"/> |
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283 </section> |
39
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284 <section name="output_options"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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285 <param name="output_selector" value="normCounts,normRLog,normVST"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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286 </section> |
27
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287 <output name="counts_out"> |
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288 <assert_contents> |
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289 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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290 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/> |
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291 </assert_contents> |
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292 </output> |
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293 <output name="rlog_out"> |
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294 <assert_contents> |
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295 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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296 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/> |
30
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297 </assert_contents> |
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298 </output> |
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299 <output name="vst_out"> |
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300 <assert_contents> |
43
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301 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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302 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*"/> |
30
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303 </assert_contents> |
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304 </output> |
27
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305 <output name="deseq_out" > |
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306 <assert_contents> |
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307 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/> |
42
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308 <has_n_lines n="3999"/> |
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309 </assert_contents> |
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310 </output> |
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311 </test> |
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312 <!--Ensure additional batch factor correction works --> |
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313 <test expect_num_outputs="2"> |
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314 <repeat name="rep_factorName"> |
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315 <param name="factorName" value="Treatment"/> |
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316 <repeat name="rep_factorLevel"> |
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317 <param name="factorLevel" value="Treated"/> |
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318 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
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319 </repeat> |
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320 <repeat name="rep_factorLevel"> |
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321 <param name="factorLevel" value="Untreated"/> |
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322 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
66203279224f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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323 </repeat> |
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324 </repeat> |
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325 <param name="batch_factors" value="batch_factors.tab"/> |
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326 <section name="advanced_options"> |
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327 <param name="use_beta_priors" value="1"/> |
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328 </section> |
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329 <section name="output_options"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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330 <param name="output_selector" value="normCounts"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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331 </section> |
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332 <output name="deseq_out"> |
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333 <assert_contents> |
43
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334 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149"/> |
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335 </assert_contents> |
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336 </output> |
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337 </test> |
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338 <!-- Same as above, but without beta priors --> |
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339 <test expect_num_outputs="2"> |
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340 <repeat name="rep_factorName"> |
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341 <param name="factorName" value="Treatment"/> |
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342 <repeat name="rep_factorLevel"> |
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343 <param name="factorLevel" value="Treated"/> |
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344 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
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345 </repeat> |
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346 <repeat name="rep_factorLevel"> |
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347 <param name="factorLevel" value="Untreated"/> |
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348 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
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349 </repeat> |
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350 </repeat> |
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351 <param name="batch_factors" value="batch_factors.tab"/> |
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352 <section name="advanced_options"> |
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353 <param name="use_beta_priors" value="0"/> |
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354 </section> |
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355 <section name="output_options"> |
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356 <param name="output_selector" value="normCounts"/> |
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357 </section> |
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358 <output name="deseq_out"> |
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359 <assert_contents> |
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360 <has_text_matching expression="FBgn0003360\t1933.*\t-3.*\t0.1.*\t-26.*\t6.*-151\t1.*-147"/> |
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361 </assert_contents> |
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362 </output> |
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363 </test> |
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364 <!--Ensure counts files without header works --> |
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365 <test expect_num_outputs="4"> |
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366 <repeat name="rep_factorName"> |
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367 <param name="factorName" value="Treatment"/> |
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368 <repeat name="rep_factorLevel"> |
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369 <param name="factorLevel" value="Treated"/> |
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370 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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371 </repeat> |
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372 <repeat name="rep_factorLevel"> |
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373 <param name="factorLevel" value="Untreated"/> |
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374 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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375 </repeat> |
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376 </repeat> |
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377 <param name="header" value="False"/> |
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378 <section name="advanced_options"> |
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379 <param name="use_beta_priors" value="1"/> |
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380 </section> |
39
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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381 <section name="output_options"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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382 <param name="output_selector" value="normCounts,normRLog,normVST"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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383 </section> |
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384 <output name="counts_out"> |
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385 <assert_contents> |
43
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386 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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387 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/> |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff
changeset
|
388 </assert_contents> |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff
changeset
|
389 </output> |
30
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
390 <output name="rlog_out"> |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
391 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
392 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
393 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/> |
30
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
394 </assert_contents> |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
395 </output> |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
396 <output name="vst_out"> |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
397 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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diff
changeset
|
398 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
399 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*"/> |
30
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
400 </assert_contents> |
3b9af9a27b5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents:
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diff
changeset
|
401 </output> |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
402 <output name="deseq_out" > |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
403 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
404 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/> |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
405 </assert_contents> |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
406 </output> |
17
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
407 </test> |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
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|
408 <!--Ensure Sailfish/Salmon input with tx2gene table works--> |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
409 <test expect_num_outputs="1"> |
17
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
410 <repeat name="rep_factorName"> |
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
411 <param name="factorName" value="Treatment"/> |
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
412 <repeat name="rep_factorLevel"> |
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
413 <param name="factorLevel" value="Treated"/> |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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414 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
17
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
415 </repeat> |
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
416 <repeat name="rep_factorLevel"> |
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
417 <param name="factorLevel" value="Untreated"/> |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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diff
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418 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
17
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
419 </repeat> |
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
420 </repeat> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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changeset
|
421 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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changeset
|
422 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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changeset
|
423 </section> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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diff
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424 <section name="output_options"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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changeset
|
425 <param name="output_selector" value=""/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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426 </section> |
17
24930eeff731
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
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diff
changeset
|
427 <param name="tximport_selector" value="tximport"/> |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
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|
428 <param name="txtype" value="sailfish"/> |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
429 <param name="mapping_format_selector" value="tabular"/> |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
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|
430 <param name="tabular_file" value="tx2gene.tab"/> |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
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431 <output name="deseq_out" > |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
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432 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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changeset
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433 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*"/> |
31
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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434 </assert_contents> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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changeset
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435 </output> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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436 </test> |
32
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
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437 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works--> |
31
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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changeset
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438 <test expect_num_outputs="1"> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
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439 <repeat name="rep_factorName"> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
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440 <param name="factorName" value="Treatment"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
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441 <repeat name="rep_factorLevel"> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
|
442 <param name="factorLevel" value="Treated"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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|
443 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
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444 </repeat> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
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445 <repeat name="rep_factorLevel"> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
|
446 <param name="factorLevel" value="Untreated"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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|
447 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
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448 </repeat> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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changeset
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449 </repeat> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
450 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
451 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
452 </section> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
453 <section name="output_options"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
454 <param name="output_selector" value=""/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
455 </section> |
31
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
|
456 <param name="tximport_selector" value="tximport"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
|
457 <param name="txtype" value="sailfish"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
|
458 <param name="mapping_format_selector" value="gtf"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
|
459 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/> |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
|
460 <output name="deseq_out" > |
7a189a7634c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
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diff
changeset
|
461 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
462 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*"/> |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
463 </assert_contents> |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
464 </output> |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
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diff
changeset
|
465 </test> |
32
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
466 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works--> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
467 <test expect_num_outputs="1"> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
468 <repeat name="rep_factorName"> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
469 <param name="factorName" value="Treatment"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
470 <repeat name="rep_factorLevel"> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
471 <param name="factorLevel" value="Treated"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
472 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
473 </repeat> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
474 <repeat name="rep_factorLevel"> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
475 <param name="factorLevel" value="Untreated"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
476 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
477 </repeat> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
478 </repeat> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
479 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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changeset
|
480 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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changeset
|
481 </section> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
482 <section name="output_options"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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changeset
|
483 <param name="output_selector" value=""/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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changeset
|
484 </section> |
32
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
485 <param name="tximport_selector" value="tximport"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
486 <param name="txtype" value="sailfish"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
487 <param name="mapping_format_selector" value="gtf"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
|
488 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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diff
changeset
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489 <output name="deseq_out" > |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
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490 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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changeset
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491 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*"/> |
32
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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492 </assert_contents> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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493 </output> |
13f324f9cdb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents:
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494 </test> |
34
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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495 <!--Ensure group tags can be used to select factor levels --> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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changeset
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496 <test expect_num_outputs="1"> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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changeset
|
497 <param name="select_data|how" value="group_tags"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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changeset
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498 <param name="select_data|countsFile"> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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changeset
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499 <collection type="list"> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
500 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
501 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
502 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
503 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
504 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
505 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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506 </collection> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
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changeset
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507 </param> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
508 <repeat name="rep_factorName"> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
509 <param name="factorName" value="Treatment"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
510 <repeat name="rep_factorLevel"> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
511 <param name="factorLevel" value="Treated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
512 <param name="groups" value="primary:treated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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changeset
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513 </repeat> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
514 <repeat name="rep_factorLevel"> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
515 <param name="factorLevel" value="Untreated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
516 <param name="groups" value="primary:untreated"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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changeset
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517 </repeat> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
518 </repeat> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
519 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
520 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
521 </section> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
522 <section name="output_options"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
523 <param name="output_selector" value=""/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
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diff
changeset
|
524 </section> |
34
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
525 <param name="tximport_selector" value="tximport"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
526 <param name="txtype" value="sailfish"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
527 <param name="mapping_format_selector" value="tabular"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
528 <param name="tabular_file" value="tx2gene.tab"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
529 <output name="deseq_out" > |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
530 <assert_contents> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
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|
531 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
532 </assert_contents> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
533 </output> |
f98981133ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents:
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diff
changeset
|
534 </test> |
36
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
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diff
changeset
|
535 <!--Ensure many_contrasts produces output collection --> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
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diff
changeset
|
536 <test expect_num_outputs="1"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
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diff
changeset
|
537 <param name="select_data|how" value="group_tags"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
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diff
changeset
|
538 <param name="select_data|countsFile"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
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diff
changeset
|
539 <collection type="list"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
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diff
changeset
|
540 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
541 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
542 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
543 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
544 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
545 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
546 </collection> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
547 </param> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
548 <repeat name="rep_factorName"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
549 <param name="factorName" value="Treatment"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
550 <repeat name="rep_factorLevel"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
551 <param name="factorLevel" value="Treated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
552 <param name="groups" value="primary:treated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
553 </repeat> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
554 <repeat name="rep_factorLevel"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
555 <param name="factorLevel" value="Untreated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
556 <param name="groups" value="primary:untreated"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
557 </repeat> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
558 </repeat> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
559 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
560 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
561 </section> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
562 <section name="output_options"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
563 <param name="output_selector" value="many_contrasts"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
564 </section> |
36
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
565 <param name="tximport_selector" value="tximport"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
566 <param name="txtype" value="sailfish"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
567 <param name="mapping_format_selector" value="tabular"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
568 <param name="tabular_file" value="tx2gene.tab"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
569 <output_collection name="split_output" type="list" count="1"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
570 <element name="Treatment_Treated_vs_Untreated"> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
571 <assert_contents> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
572 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
573 </assert_contents> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
574 </element> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
575 </output_collection> |
d9f48120c02b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents:
34
diff
changeset
|
576 </test> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
577 <!--Test alpha_ma option--> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
578 <test expect_num_outputs="1"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
579 <repeat name="rep_factorName"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
580 <param name="factorName" value="Treatment"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
581 <repeat name="rep_factorLevel"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
582 <param name="factorLevel" value="Treated"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
583 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
584 </repeat> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
585 <repeat name="rep_factorLevel"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
586 <param name="factorLevel" value="Untreated"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
587 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
588 </repeat> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
589 </repeat> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
590 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
591 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
592 </section> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
593 <section name="output_options"> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
594 <param name="output_selector" value=""/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
595 <param name="alpha_ma" value="0.05"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
596 </section> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
597 <param name="tximport_selector" value="tximport"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
598 <param name="txtype" value="sailfish"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
599 <param name="mapping_format_selector" value="gtf"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
600 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
601 <output name="deseq_out" > |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
602 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
603 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*"/> |
39
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
604 </assert_contents> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
605 </output> |
b30a443484ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents:
38
diff
changeset
|
606 </test> |
41
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
607 <!-- Same as above alpha_ma test, but with size factors --> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
608 <test expect_num_outputs="2"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
609 <repeat name="rep_factorName"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
610 <param name="factorName" value="Treatment"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
611 <repeat name="rep_factorLevel"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
612 <param name="factorLevel" value="Treated"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
613 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
614 </repeat> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
615 <repeat name="rep_factorLevel"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
616 <param name="factorLevel" value="Untreated"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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changeset
|
617 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
618 </repeat> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
619 </repeat> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
620 <section name="output_options"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
621 <param name="output_selector" value="sizefactors"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
622 <param name="alpha_ma" value="0.05"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
623 </section> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
624 <param name="tximport_selector" value="tximport"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
625 <param name="txtype" value="sailfish"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
626 <param name="mapping_format_selector" value="gtf"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
627 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
628 <output name="sizefactors_out"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
629 <assert_contents> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
630 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
631 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
632 </assert_contents> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
633 </output> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
634 </test> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
635 <!--Test alpha_ma option, but with user-provided size factors --> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
636 <test expect_num_outputs="1"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
637 <repeat name="rep_factorName"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
638 <param name="factorName" value="Treatment"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
639 <repeat name="rep_factorLevel"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
640 <param name="factorLevel" value="Treated"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
641 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
642 </repeat> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
643 <repeat name="rep_factorLevel"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
644 <param name="factorLevel" value="Untreated"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
645 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
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646 </repeat> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
647 </repeat> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
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648 <section name="advanced_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
649 <param name="use_beta_priors" value="1"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
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650 <conditional name="esf_cond"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
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651 <param name="esf" value="user"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
652 <param name="size_factor_input" value="size_factors_out.tsv"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
653 </conditional> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
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654 </section> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
655 <section name="output_options"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
656 <param name="output_selector" value=""/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
657 <param name="alpha_ma" value="0.05"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
658 </section> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
659 <param name="tximport_selector" value="tximport"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
660 <param name="txtype" value="sailfish"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
661 <param name="mapping_format_selector" value="gtf"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
42
diff
changeset
|
662 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
663 <output name="deseq_out"> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
664 <assert_contents> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
665 <has_text_matching expression="ENSG00000168671\t1.90.*\t-0.05.*\t0.75.*\t-0.07.*\t0.94.*\t0.95.*"/> |
41
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
666 </assert_contents> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
667 </output> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
668 </test> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
669 <!-- Same as above alpha_ma size factor test, but with a non-default estimator--> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
670 <test expect_num_outputs="2"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
671 <repeat name="rep_factorName"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
672 <param name="factorName" value="Treatment"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
673 <repeat name="rep_factorLevel"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
674 <param name="factorLevel" value="Treated"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
675 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
676 </repeat> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
677 <repeat name="rep_factorLevel"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
678 <param name="factorLevel" value="Untreated"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
679 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
680 </repeat> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
681 </repeat> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
682 <section name="advanced_options"> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
683 <param name="esf" value="poscounts"/> |
41
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
684 </section> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
685 <section name="output_options"> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
686 <param name="output_selector" value="sizefactors"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
687 <param name="alpha_ma" value="0.05"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
688 </section> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
689 <param name="tximport_selector" value="tximport"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
690 <param name="txtype" value="sailfish"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
691 <param name="mapping_format_selector" value="gtf"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
692 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
40
diff
changeset
|
693 <output name="sizefactors_out" > |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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694 <assert_contents> |
43
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|
695 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+"/> |
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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|
696 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+"/> |
41
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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|
697 </assert_contents> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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698 </output> |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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|
699 </test> |
42
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff
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|
700 <!--Test prefilter parameter --> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
701 <test expect_num_outputs="2"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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41
diff
changeset
|
702 <repeat name="rep_factorName"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
703 <param name="factorName" value="Treatment"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff
changeset
|
704 <repeat name="rep_factorLevel"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff
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|
705 <param name="factorLevel" value="Treated"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
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diff
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|
706 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
707 </repeat> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
41
diff
changeset
|
708 <repeat name="rep_factorLevel"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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changeset
|
709 <param name="factorLevel" value="Untreated"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
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diff
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|
710 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
41
diff
changeset
|
711 </repeat> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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diff
changeset
|
712 </repeat> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff
changeset
|
713 <section name="advanced_options"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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diff
changeset
|
714 <conditional name="prefilter_conditional"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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diff
changeset
|
715 <param name="prefilter" value="-P"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
716 <param name="prefilter_value" value="10"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
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diff
changeset
|
717 </conditional> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff
changeset
|
718 </section> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
719 <section name="output_options"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff
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|
720 <param name="output_selector" value="normCounts"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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|
721 </section> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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diff
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|
722 <output name="counts_out"> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
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diff
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|
723 <assert_contents> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
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diff
changeset
|
724 <has_n_lines n="2922"/> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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diff
changeset
|
725 </assert_contents> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
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diff
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|
726 </output> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents:
41
diff
changeset
|
727 <output name="deseq_out" > |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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diff
changeset
|
728 <assert_contents> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents:
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|
729 <has_n_lines n="2921"/> <!-- Smallen value when compared with the first test--> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
730 </assert_contents> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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changeset
|
731 </output> |
6ef2cba4e35a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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|
732 </test> |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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changeset
|
733 </tests> |
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|
734 <help><![CDATA[ |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
735 .. class:: infomark |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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changeset
|
736 |
15
d856341e03c8
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|
737 **What it does** |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
738 |
43
621ddf5967d2
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|
739 Uses DESeq2 version @DESEQ2_VERSION@ to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
740 |
23
d1241c2b81a7
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|
741 ----- |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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742 |
0
5b1ce9db498e
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743 **Inputs** |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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744 |
23
d1241c2b81a7
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745 **Count Files** |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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746 |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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|
747 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level. |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
748 |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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749 The following table gives some examples of factors and their levels: |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
750 |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
751 ========= ============== =============== |
15
d856341e03c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1
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752 Factor Factor level 1 Factor level 2 |
0
5b1ce9db498e
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753 --------- -------------- --------------- |
5b1ce9db498e
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|
754 Treatment Treated Untreated |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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755 --------- -------------- --------------- |
5b1ce9db498e
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|
756 Condition Knockdown Wildtype |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
757 --------- -------------- --------------- |
5b1ce9db498e
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changeset
|
758 TimePoint Day4 Day1 |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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759 --------- -------------- --------------- |
5b1ce9db498e
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|
760 SeqType SingleEnd PairedEnd |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
761 --------- -------------- --------------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
762 Gender Female Male |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
763 ========= ============== =============== |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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changeset
|
764 |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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765 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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|
766 |
27
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|
767 DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. |
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768 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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769 **Salmon or Sailfish Files** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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|
770 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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771 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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|
772 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
773 Example: |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
774 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
775 ============ ========== =============== =========== =========== |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
776 Name Length EffectiveLength TPM NumReads |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
777 ------------ ---------- --------------- ----------- ----------- |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
778 NR_001526 164 20.4518 0 0 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
779 NR_001526_1 164 20.4518 0 0 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
780 NR_001526_2 164 20.4518 0 0 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
781 NM_130786 1764 1956.04 2.47415 109.165 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
782 NR_015380 2129 2139.53 1.77331 85.5821 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
783 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
784 NM_001198819 9527 7964.62 0 0 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
785 NM_001198820 9410 7855.78 0 0 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
786 NM_014576 9267 7714.88 0.0481114 8.37255 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
787 ============ ========== =============== =========== =========== |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
788 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
789 **kallisto Files** |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
790 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
791 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below. |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
792 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
793 Example: |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
794 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
795 ============ ========== =============== =========== =========== |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
796 target_id length eff_length est_counts tpm |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
797 ------------ ---------- --------------- ----------- ----------- |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
798 NR_001526 164 20.4518 0 0 |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
799 NR_001526_1 164 20.4518 0 0 |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
800 NR_001526_2 164 20.4518 0 0 |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
801 NM_130786 1764 1956.04 109.165 2.47415 |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
802 NR_015380 2129 2139.53 85.5821 1.77331 |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
803 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07 |
27
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
804 NM_001198819 9527 7964.62 0 0 |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
805 NM_001198820 9410 7855.78 0 0 |
dc6bc19f05ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
26
diff
changeset
|
806 NM_014576 9267 7714.88 8.37255 0.0481114 |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
22
diff
changeset
|
807 ============ ========== =============== =========== =========== |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
808 |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
809 ----- |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
810 |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
811 **Output** |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
812 |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
813 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF. |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
814 |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
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changeset
|
815 ====== ========================================================== |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
816 Column Description |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
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changeset
|
817 ------ ---------------------------------------------------------- |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
818 1 Gene Identifiers |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
819 2 mean normalised counts, averaged over all samples from both conditions |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
820 3 the logarithm (to basis 2) of the fold change (See the note in inputs section) |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
821 4 standard error estimate for the log2 fold change estimate |
13
00ff49f9e750
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents:
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diff
changeset
|
822 5 Wald statistic |
00ff49f9e750
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents:
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diff
changeset
|
823 6 p value for the statistical significance of this change |
00ff49f9e750
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents:
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diff
changeset
|
824 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
825 which controls false discovery rate (FDR) |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
826 ====== ========================================================== |
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff
changeset
|
827 |
41
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
828 By selecting ``Output sample size factors`` in the "Output options" |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
829 selection box, the size factors used to normalize the samples can also |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
830 be output as a tabular file. |
0a0a3388e3f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents:
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diff
changeset
|
831 |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
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changeset
|
832 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html |
23
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
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|
833 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html |
d1241c2b81a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
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diff
changeset
|
834 ]]></help> |
43
621ddf5967d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents:
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diff
changeset
|
835 <expand macro="citations"/> |
0
5b1ce9db498e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
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changeset
|
836 </tool> |