Mercurial > repos > iuc > trinity
annotate run_DE_analysis.xml @ 8:258c64019e50 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a
author | iuc |
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date | Tue, 28 Jun 2016 12:22:40 -0400 |
parents | 1b7800489efb |
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rev | line source |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
iuc
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1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1.1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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2 <description>using a Trinity assembly</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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3 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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4 <requirement type="package" version="2.1.1">trinity</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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6 <requirement type="package" version="1.10.0">deseq2</requirement> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> |
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1b7800489efb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352
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8 <requirement type="package" version="3.14.0">bioconductor-edger</requirement> |
1b7800489efb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352
iuc
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9 <requirement type="package" version="3.28.10">bioconductor-limma</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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10 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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11 <stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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12 <exit_code range="1:"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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13 </stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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14 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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15 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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16 ln -s "${matrix}" "input.matrix" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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17 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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18 && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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19 |
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de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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20 run_DE_analysis.pl |
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692491de7df5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
iuc
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21 |
2
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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22 --matrix "input.matrix" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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23 |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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24 --samples_file "${samples}" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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25 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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26 --method ${method_choice.method} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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27 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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28 #if $method_choice.method == "edgeR": |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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29 --dispersion ${method_choice.edger_dispersion} |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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30 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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31 |
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de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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32 #if $method_choice.method == "ROTS": |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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33 --ROTS_B ${method_choice.rots_b} |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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34 --ROTS_K ${method_choice.rots_k} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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35 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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36 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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37 --min_rowSum_counts ${additional_params.min_rowSum_counts} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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38 |
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de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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39 #if $additional_params.reference_sample: |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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40 --reference_sample ${additional_params.reference_sample} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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41 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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42 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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43 #if $additional_params.contrasts: |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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44 --contrasts ${additional_params.contrasts} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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45 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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46 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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47 --output results |
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48 |
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49 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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50 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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51 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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52 <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
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53 |
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54 <conditional name="method_choice"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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55 <param type="select" name="method" label="Differential analysis method"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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56 <option value="edgeR">edgeR</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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57 <option value="DESeq2">DESeq2</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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58 <option value="voom">voom</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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59 <option value="ROTS">ROTS</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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60 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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61 <when value="edgeR"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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62 <param name="edger_dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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63 </when> |
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64 <when value="ROTS"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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65 <param name="rots_b" type="integer" value="500" label="number of bootstraps and permutation resampling" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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66 <param name="rots_k" type="integer" value="5000" label="largest top genes size" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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67 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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68 <when value="voom"> |
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69 </when> |
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70 <when value="DESeq2"> |
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71 </when> |
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72 </conditional> |
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73 |
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74 <section name="additional_params" title="Additional Options" expanded="False"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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75 <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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76 <param name="reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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77 <param format="tabular" name="contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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78 </section> |
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79 </inputs> |
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80 <outputs> |
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81 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}"> |
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82 <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" /> |
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83 </collection> |
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84 <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}"> |
8
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85 <discover_datasets pattern="(?P<name>.+)\.pdf$" ext="pdf" directory="results" /> |
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86 </collection> |
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87 </outputs> |
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88 <tests> |
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89 <test> |
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90 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> |
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91 <param name="samples" value="count/samples.txt"/> |
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92 <param name="method" value="DESeq2"/> |
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93 <output_collection name="DE_results"> |
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94 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/> |
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95 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/> |
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96 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/> |
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97 </output_collection> |
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98 <output_collection name="PDF_results"> |
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99 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/> |
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100 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> |
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101 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> |
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102 </output_collection> |
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103 </test> |
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104 </tests> |
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105 <help> |
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106 <![CDATA[ |
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107 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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108 This tool performs differential expression analyses on a transcriptome assembled with Trinity. |
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109 |
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110 **Inputs** |
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111 |
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112 This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool. |
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113 |
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114 You must describe your samples and replicates with a tabular file looking like this: |
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115 |
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116 =========== ================ |
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117 ConditionA CondA_replicate1 |
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118 ----------- ---------------- |
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119 ConditionA CondA_replicate2 |
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120 ----------- ---------------- |
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121 ConditionB CondB_replicate1 |
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122 ----------- ---------------- |
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123 ConditionB CondB_replicate2 |
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124 ----------- ---------------- |
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125 ConditionC CondC_replicate1 |
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126 ----------- ---------------- |
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127 ConditionC CondC_replicate2 |
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128 ----------- ---------------- |
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129 ConditionC CondC_replicate3 |
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130 =========== ================ |
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131 |
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132 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'. |
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133 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'. |
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134 |
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135 |
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136 .. _Trinity: http://trinityrnaseq.github.io |
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137 ]]> |
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138 </help> |
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139 |
2
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140 <citations> |
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141 <citation type="doi">10.1038/nbt.1883</citation> |
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142 </citations> |
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143 </tool> |
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144 |