Mercurial > repos > iuc > trinity
annotate abundance_estimates_to_matrix.xml @ 7:1b7800489efb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352
author | iuc |
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date | Mon, 20 Jun 2016 11:44:50 -0400 |
parents | e4a9e0798360 |
children | 258c64019e50 |
rev | line source |
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2
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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changeset
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1 <tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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2 <description>for a de novo assembly of RNA-Seq data by Trinity</description> |
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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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3 <requirements> |
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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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4 <requirement type="package" version="2.1.1">trinity</requirement> |
7
1b7800489efb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352
iuc
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5 <requirement type="package" version="3.14.0">bioconductor-edger</requirement> |
2
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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6 </requirements> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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7 <stdio> |
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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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8 <exit_code range="1:"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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9 </stdio> |
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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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10 <command><![CDATA[ |
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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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11 #for $entry in $samples: |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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12 ln -s "${entry.file}" "${entry.sample_name}.tsv" && |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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13 #end for |
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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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14 |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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15 abundance_estimates_to_matrix.pl |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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16 |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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17 --est_method ${est_method} |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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18 --cross_sample_norm ${additional_params.cross_sample_norm} |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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19 |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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diff
changeset
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20 #for $entry in $samples: |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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21 "${entry.sample_name}.tsv" |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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22 #end for |
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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 ]]></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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changeset
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24 <inputs> |
3
c7555bc21812
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
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25 <repeat name="samples" title="Abundance estimates for samples"> |
2
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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26 <param name="file" label="Add file" type="data" format="tabular"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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27 <param name="sample_name" label="Sample name" type="text"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents:
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28 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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29 </param> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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30 </repeat> |
3
c7555bc21812
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
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2
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31 |
2
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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32 <param type="select" name="est_method" label="Abundance estimation method"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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33 <option value="RSEM">RSEM</option> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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34 <option value="eXpress">eXpress</option> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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35 </param> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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36 |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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37 <section name="additional_params" title="Additional Options" expanded="False"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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38 <param type="select" name="cross_sample_norm" label="Cross sample normalization"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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39 <option value="TMM">TMM</option> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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40 <option value="UpperQuartile">UpperQuartile</option> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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41 <option value="none">None</option> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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42 </param> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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43 </section> |
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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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44 </inputs> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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45 <outputs> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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46 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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47 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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48 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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49 <filter>additional_params['cross_sample_norm'] == "TMM"</filter> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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50 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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51 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix"> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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52 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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53 </data> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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54 </outputs> |
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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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55 <tests> |
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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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56 <test> |
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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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57 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> |
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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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58 <param name="samples_0|sample_name" value="sample_A"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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59 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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60 <param name="samples_1|sample_name" value="sample_B"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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61 <param name="est_method" value="RSEM"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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62 <param name="cross_sample_norm" value="TMM"/> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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63 <output name="trans_counts"> |
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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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64 <assert_contents> |
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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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65 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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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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66 <has_n_columns n="3" /> |
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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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67 </assert_contents> |
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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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68 </output> |
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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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69 <output name="TPM_no_norm"> |
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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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70 <assert_contents> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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71 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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72 <has_n_columns n="3" /> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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73 </assert_contents> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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74 </output> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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75 <output name="norm"> |
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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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76 <assert_contents> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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77 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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78 <has_n_columns n="3" /> |
de0af39266ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
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79 </assert_contents> |
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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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80 </output> |
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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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81 </test> |
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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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82 <test> |
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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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83 <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/> |
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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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84 <param name="samples_0|sample_name" value="sample_A"/> |
de0af39266ef
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85 <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/> |
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86 <param name="samples_1|sample_name" value="sample_B"/> |
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87 <param name="est_method" value="RSEM"/> |
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88 <param name="cross_sample_norm" value="TMM"/> |
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89 <output name="trans_counts"> |
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90 <assert_contents> |
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91 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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92 <has_n_columns n="3" /> |
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93 </assert_contents> |
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94 </output> |
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95 <output name="TPM_no_norm"> |
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96 <assert_contents> |
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97 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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98 <has_n_columns n="3" /> |
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99 </assert_contents> |
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100 </output> |
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101 <output name="norm"> |
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102 <assert_contents> |
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103 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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104 <has_n_columns n="3" /> |
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105 </assert_contents> |
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106 </output> |
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107 </test> |
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108 <test> |
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109 <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/> |
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110 <param name="samples_0|sample_name" value="sample_A"/> |
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111 <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/> |
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112 <param name="samples_1|sample_name" value="sample_B"/> |
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113 <param name="est_method" value="eXpress"/> |
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114 <param name="cross_sample_norm" value="TMM"/> |
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115 <output name="trans_counts"> |
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116 <assert_contents> |
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117 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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118 <has_n_columns n="3" /> |
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119 </assert_contents> |
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120 </output> |
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121 <output name="TPM_no_norm"> |
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122 <assert_contents> |
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123 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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124 <has_n_columns n="3" /> |
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125 </assert_contents> |
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126 </output> |
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127 <output name="norm"> |
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128 <assert_contents> |
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129 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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130 <has_n_columns n="3" /> |
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131 </assert_contents> |
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132 </output> |
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133 </test> |
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134 <test> |
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135 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> |
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136 <param name="samples_0|sample_name" value="sample_A"/> |
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137 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> |
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138 <param name="samples_1|sample_name" value="sample_B"/> |
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139 <param name="est_method" value="RSEM"/> |
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140 <param name="cross_sample_norm" value="UpperQuartile"/> |
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141 <output name="trans_counts"> |
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142 <assert_contents> |
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143 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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144 <has_n_columns n="3" /> |
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145 </assert_contents> |
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146 </output> |
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147 <output name="TPM_no_norm"> |
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148 <assert_contents> |
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149 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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150 <has_n_columns n="3" /> |
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151 </assert_contents> |
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152 </output> |
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153 <output name="norm" file="count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix" /> |
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154 </test> |
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155 <test> |
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156 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> |
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157 <param name="samples_0|sample_name" value="sample_A"/> |
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158 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> |
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159 <param name="samples_1|sample_name" value="sample_B"/> |
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160 <param name="est_method" value="RSEM"/> |
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161 <param name="cross_sample_norm" value="none"/> |
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162 <output name="trans_counts"> |
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163 <assert_contents> |
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164 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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165 <has_n_columns n="3" /> |
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166 </assert_contents> |
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167 </output> |
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168 <output name="TPM_no_norm"> |
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169 <assert_contents> |
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170 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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171 <has_n_columns n="3" /> |
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172 </assert_contents> |
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173 </output> |
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174 </test> |
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175 </tests> |
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176 <help> |
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177 <![CDATA[ |
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178 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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179 This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file. |
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180 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools. |
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181 |
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182 **Inputs** |
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183 |
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184 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/ |
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185 Each sample must have a name, that should be used in subsequent tools. |
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186 |
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187 **Output** |
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188 |
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189 This tool will produce a single matrix file. More details on this page: |
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190 |
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191 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification |
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192 |
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193 |
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194 .. _Trinity: http://trinityrnaseq.github.io |
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195 ]]> |
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196 </help> |
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197 |
2
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198 <citations> |
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199 <citation type="doi">10.1038/nbt.1883</citation> |
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200 </citations> |
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201 </tool> |
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202 |