Mercurial > repos > davidecangelosi > pipe_t
annotate pipe-t.xml @ 29:8cb95051067d draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d3f6bd65b41ccfbfd3ae294e15122952b7e040b8
author | davidecangelosi |
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date | Thu, 06 Jun 2019 12:01:47 -0400 |
parents | 7fbfe6f424f0 |
children | 30ab487171ab |
rev | line source |
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0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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1 <?xml version="1.0"?> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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2 <tool id="pipe-t" name="PIPE-T" version="1.0" hidden="false"> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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3 <description>A tool for analyzing RTqPCR expression data </description> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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4 <requirements> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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5 <requirement type="package" version="3.5.0">r-base</requirement> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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6 <requirement type="package" version="7.2.0">libgcc</requirement> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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7 <requirement type="package" version="1.36.0">bioconductor-htqpcr</requirement> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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8 <requirement type="package" version="3.8.0">bioconductor-rankprod</requirement> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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9 <requirement type="package" version="1.56.0">bioconductor-impute</requirement> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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10 <requirement type="package" version="1.11.0">r-bbmisc</requirement> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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11 <requirement type="package" version="1.8.4">r-psych</requirement> |
1
ecd0a79e8130
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 065f5723959c01b6afec74dad189608477e0ac18
davidecangelosi
parents:
0
diff
changeset
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12 <requirement type="package" version="1.8_3">r-zoo</requirement> |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
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13 <requirement type="package" version="1.28.0">bioconductor-normqpcr </requirement> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
14 </requirements> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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15 <stdio> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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16 <exit_code range="1:" /> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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17 </stdio> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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18 <command> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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19 <![CDATA[ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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20 #for $input in $dp.list_files |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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21 ln -sf '$input' '$__tool_directory__/Symlink/${input.element_identifier}'; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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22 #end for |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
23 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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24 #if str( $dn.condNorm.normMethod ) == "deltaCt": |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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25 #if str( $dn.condNorm.deltamethod.format ) == "userdefined": |
10
bc5697f41720
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 2c7880131d5a3ca88ddc31e2a52a12fa17774178
davidecangelosi
parents:
9
diff
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26 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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27 #if str( $de.condDEA.method ) == "ttest": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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28 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
|
29 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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30 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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31 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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32 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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33 #if str( $de.condDEA.method ) == "rp": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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34 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
|
35 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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36 #if str( $de.condDEA.method ) == "none": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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37 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
|
38 #end if |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
39 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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40 |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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41 #if str( $df.condImpute.format ) == "knn": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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42 #if str( $de.condDEA.method ) == "ttest": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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43 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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44 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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45 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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46 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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47 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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48 #if str( $de.condDEA.method ) == "rp": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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49 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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50 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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51 #if str( $de.condDEA.method ) == "none": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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52 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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53 #end if |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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54 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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55 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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56 #if str( $dn.condNorm.deltamethod.format ) == "genorm": |
10
bc5697f41720
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 2c7880131d5a3ca88ddc31e2a52a12fa17774178
davidecangelosi
parents:
9
diff
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57 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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58 #if str( $de.condDEA.method ) == "ttest": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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59 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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60 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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61 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
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62 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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diff
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63 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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diff
changeset
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64 #if str( $de.condDEA.method ) == "rp": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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65 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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diff
changeset
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66 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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diff
changeset
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67 #if str( $de.condDEA.method ) == "none": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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68 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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69 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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diff
changeset
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70 #end if |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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diff
changeset
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71 |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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changeset
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72 #if str( $df.condImpute.format ) == "knn": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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changeset
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73 #if str( $de.condDEA.method ) == "ttest": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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74 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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changeset
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75 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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76 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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77 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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78 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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79 #if str( $de.condDEA.method ) == "rp": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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80 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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changeset
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81 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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changeset
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82 #if str( $de.condDEA.method ) == "none": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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83 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
changeset
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84 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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changeset
|
85 #end if |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
86 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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87 #if str( $dn.condNorm.deltamethod.format ) == "normfinder": |
10
bc5697f41720
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 2c7880131d5a3ca88ddc31e2a52a12fa17774178
davidecangelosi
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9
diff
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88 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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89 #if str( $de.condDEA.method ) == "ttest": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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90 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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diff
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91 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
parents:
11
diff
changeset
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92 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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93 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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diff
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94 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
changeset
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95 #if str( $de.condDEA.method ) == "rp": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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96 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
changeset
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97 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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98 #if str( $de.condDEA.method ) == "none": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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99 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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diff
changeset
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100 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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101 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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102 |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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103 #if str( $df.condImpute.format ) == "knn": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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104 #if str( $de.condDEA.method ) == "ttest": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
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105 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
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106 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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11
diff
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107 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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108 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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109 #end if |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
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110 #if str( $de.condDEA.method ) == "rp": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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111 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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112 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
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113 #if str( $de.condDEA.method ) == "none": |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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114 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
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115 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
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diff
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116 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
davidecangelosi
parents:
1
diff
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117 #end if |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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118 |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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119 #else |
10
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 2c7880131d5a3ca88ddc31e2a52a12fa17774178
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120 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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diff
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121 #if str( $de.condDEA.method ) == "ttest": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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122 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
123 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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124 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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125 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
davidecangelosi
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126 #end if |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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127 #if str( $de.condDEA.method ) == "rp": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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128 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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129 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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130 #if str( $de.condDEA.method ) == "none": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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131 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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132 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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133 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
diff
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134 |
185ba61836ab
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135 #if str( $df.condImpute.format ) == "knn": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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136 #if str( $de.condDEA.method ) == "ttest": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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137 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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138 #end if |
18
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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139 #if str( $de.condDEA.method ) == "wtest": |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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140 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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141 #end if |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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142 #if str( $de.condDEA.method ) == "rp": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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143 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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diff
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144 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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diff
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145 #if str( $de.condDEA.method ) == "none": |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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146 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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147 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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148 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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149 #end if |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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150 ]]> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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151 </command> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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152 <inputs> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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153 <section name="dp" title="File uploading and parsing" expanded="true"> |
11
d6e062f6d462
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit bbd56a469f814565939ff5467a35121658f26133
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154 <param name="list_files" type="data_collection" collection_type="list" value="" label="Select a collection list from the history tab" help="Collection should be of category List. "/> |
d6e062f6d462
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit bbd56a469f814565939ff5467a35121658f26133
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155 <param name="files" type="data" format="txt" label="Select one of the files from the history tab" help="File should contains only the columns: sampleName and Treatment." /> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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156 <param name="formatFile" type="select" label="Select one of the file formats from the list below." help=""> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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157 <option value="EDS" selected="true">EDS</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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158 <option value="SDS" >SDS</option> |
28
7fbfe6f424f0
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 35cbb03a7d2f13985cda31d23e0ed318bf65d068
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159 <option value="OpenArray" >OpenArray</option> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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160 <option value="LightCycler" >LightCycler</option> |
28
7fbfe6f424f0
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 35cbb03a7d2f13985cda31d23e0ed318bf65d068
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161 <option value="CFX">CFX</option> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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162 <option value="BioMark" >BioMark</option> |
28
7fbfe6f424f0
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 35cbb03a7d2f13985cda31d23e0ed318bf65d068
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163 <option value="plain">Plain</option> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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164 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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165 <param name="n" type="integer" min="1" max="1000" value="384" label="Type the number of transcripts in your file" /> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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166 </section> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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167 <section name="dc" title="Ct filtering and categorization" expanded="true"> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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168 <param name="Ctmin" type="integer" min="0" max="40" value="14" label="Set up a minimum Ct value" |
185ba61836ab
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169 help="Any Ct below your selected value will be labelled as Unreliable." /> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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170 <param name="Ctmax" type="integer" min="0" max="40" value="32" label="Set up a maximum Ct value" |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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171 help="Any Ct above your selected value will be labelled as Unreliable."/> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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172 <param name="flag" type="select" label="Select TRUE if you want that PIPE-T assigns category 'Unreliable' on the basis of FAILURE flag" help="Data in qPCRset objects will have feature categories (Unreliable, Undetermined) assigned to them based on different Ct criteria."> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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173 <option value="TRUE">TRUE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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174 <option value="FALSE">FALSE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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175 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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|
176 </section> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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177 <section name="dn" title="Normalization" expanded="true"> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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178 <conditional name="condNorm"> |
11
d6e062f6d462
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179 <param name="normMethod" type="select" label="Select one of the normalization methods from the list below." help="Normalization is important to reduce technical variability in the data."> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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180 <option value="globalmean" selected="true">Global mean</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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181 <option value="deltaCt">DeltaCt method (housekeeping genes)</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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182 <option value="geometric.mean">Modified global mean</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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183 <option value="quantile">Quantile</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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184 <option value="norm.rankinvariant">Rank invariant</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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185 <option value="scale.rankinvariant">Scale rank invariant</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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186 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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187 <when value="deltaCt"> |
9
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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parents:
1
diff
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188 <conditional name="deltamethod"> |
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189 <param name="format" type="select" label="Select one of the methods from the list below for selecting normalizers." help=""> |
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190 <option value="userdefined" selected="true">User defined</option> |
69f5c4d6e6bd
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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191 <option value="genorm">geNorm</option> |
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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192 <option value="normfinder">NormFinder</option> |
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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193 </param> |
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7664e4dc44eb4f141ffd01627ee66858cc9887ff
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194 <when value="userdefined"> |
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195 <param name="normalizers" type="text" label="Type a comma separated list of housekeeping transcripts that will be used as normalizers." value="U6 snRNA-001973"></param> |
9
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196 </when> |
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197 <when value="genorm"> |
11
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198 <param name="minhkgenorm" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by geNorm method." value="2"></param> |
9
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199 </when> |
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200 <when value="normfinder"> |
11
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201 <param name="minhknormfinder" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by NormFinder method." value="1"></param> |
9
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202 </when> |
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203 </conditional> |
0
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204 </when> |
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205 </conditional> |
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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206 </section> |
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207 <section name="df" title="Transcript filtering and imputation" expanded="true"> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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208 <param name="percent" type="integer" min="0" max="100" value="0" label="Set up a percentage of NAs." |
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209 help="Transcripts with more than the specified percentage of NAs across all samples will be removed." /> |
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210 <param name="filtname" type="text" label="Type a comma separeted list of transcript identifiers to filter out" help="Transcript identifiers specified in the List will be removed." value="U6 snRNA-001973,hsa-miR-520a"> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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211 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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212 <conditional name="condImpute"> |
185ba61836ab
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213 <param name="format" type="select" label="Select one of the imputation methods from the list below." help=""> |
185ba61836ab
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214 <option value="mestdagh" selected="true">Mestdagh</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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215 <option value="knn">K-Nearest Neighbour</option> |
185ba61836ab
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216 <option value="cubic">Cubic Spline</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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217 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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218 <when value="knn"> |
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219 <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use in the KNN imputation method" /> |
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220 <param name="maxp" type="integer" min="1" max="2000" value="1500" label="Type the maximum number of imputed transcripts to use in the KNN method." help="Larger numbers are divided by two-means clustering (recursively) |
0
185ba61836ab
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221 prior to imputation. "/> |
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222 </when> |
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223 </conditional> |
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224 </section> |
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225 <section name="de" title="Differential expression analysis" expanded="true"> |
185ba61836ab
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226 <conditional name="condDEA"> |
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227 <param name="method" type="select" label="Select one of the methods from the list below or NONE."> |
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228 |
0
185ba61836ab
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229 <option value="ttest" selected="true">T-test and fold change</option> |
18
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230 <option value="wtest" selected="true"> Two sample Wilcoxon test and fold change</option> |
0
185ba61836ab
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231 <option value="rp">Rank Product (Only for unpaired data)</option> |
185ba61836ab
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232 <option value="none">NONE</option> |
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233 </param> |
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234 <when value="ttest"> |
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235 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance."> |
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236 <option value="two.sided" selected="true">Two sided</option> |
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237 <option value="greater">Greater</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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238 <option value="less">Lower</option> |
185ba61836ab
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239 </param> |
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240 <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file"> |
0
185ba61836ab
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241 <option value="TRUE" >TRUE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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242 <option value="FALSE" selected="true">FALSE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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243 </param> |
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244 <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately."> |
0
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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245 <option value="TRUE" selected="true">TRUE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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246 <option value="FALSE" >FALSE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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247 </param> |
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248 <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help=""> |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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249 <option value="TRUE" selected="true">TRUE</option> |
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250 <option value="FALSE" >FALSE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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251 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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252 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and |
185ba61836ab
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253 biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined."> |
185ba61836ab
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254 <option value="TRUE" selected="true">TRUE</option> |
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255 <option value="FALSE" >FALSE</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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256 </param> |
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257 <param name="padjust" type="select" label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing"> |
0
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258 <option value="BH" selected="true">Benjamini-Hochberg</option> |
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259 <option value="bonferroni">Bonferroni</option> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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260 </param> |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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261 </when> |
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262 <when value="wtest"> |
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263 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance."> |
2a6088c11d42
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264 <option value="two.sided" selected="true">Two sided</option> |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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265 <option value="greater">Greater</option> |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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266 <option value="less">Lower</option> |
2a6088c11d42
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
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267 </param> |
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268 <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file"> |
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269 <option value="TRUE" >TRUE</option> |
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270 <option value="FALSE" selected="true">FALSE</option> |
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271 </param> |
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272 <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately."> |
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273 <option value="TRUE" selected="true">TRUE</option> |
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274 <option value="FALSE" >FALSE</option> |
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275 </param> |
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276 <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help=""> |
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277 <option value="TRUE" selected="true">TRUE</option> |
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278 <option value="FALSE" >FALSE</option> |
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279 </param> |
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280 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and |
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281 biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined."> |
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282 <option value="TRUE" selected="true">TRUE</option> |
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283 <option value="FALSE" >FALSE</option> |
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284 </param> |
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285 <param name="padjust" type="select" label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing"> |
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286 <option value="BH" selected="true">Benjamini-Hochberg</option> |
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287 <option value="bonferroni">Bonferroni</option> |
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288 </param> |
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289 </when> |
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290 <when value="rp"> |
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291 </when> |
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292 </conditional> |
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293 </section> |
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294 </inputs> |
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295 <outputs> |
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296 <data format="txt" name="galaxy_output1" label="1_Ct_Raw"/> |
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297 <data format="png" name="galaxy_output2" label="2_Boxplot after data categorization"/> |
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298 <data format="txt" name="galaxy_output3" label="3_Normalized data"/> |
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299 <data format="png" name="galaxy_output4" label="4_ECDF"/> |
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300 <data format="png" name="galaxy_output6" label="5_Boxplot after data normalization"/> |
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301 <data format="txt" name="galaxy_output5" label="6_Imputed data"/> |
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302 <data format="txt" name="galaxy_output7" label="7_Differentially Expressed transcripts"/> |
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303 </outputs> |
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304 |
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305 <help> |
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306 <![CDATA[ |
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307 **What it does** |
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308 INPUTS: This tool parses a list of RT-qPCR file and a file associating these files and one of two groups |
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309 OUTPUTS: and returs |
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310 1) A txt file with the raw Ct data |
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311 2) A PNG file of a boxplot with the Ct data after data categorization for each sample |
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312 3) A txt file with normalized data |
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313 4) A PNG file with the Empirical cumulative distribution before and after data normalization |
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314 5) A PNG file of a boxplot with the normalzied data for each sample |
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315 6) A txt file with imputed data for each missing value |
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316 7) A txt file with the results of the differntial expression analyis |
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317 ]]> |
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318 </help> |
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319 </tool> |