Mercurial > repos > thanhlv > biotradis
annotate biotradis_tradis_comparison.xml @ 7:09c1f97a5bcc draft
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
| author | thanhlv |
|---|---|
| date | Fri, 06 Dec 2019 10:11:20 -0500 |
| parents | 5506c4307812 |
| children |
| rev | line source |
|---|---|
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
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1 <tool id="tradis_comparison" name="tradis comparison" version="@VERSION@"> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
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2 <description>Compares two experimental conditions</description> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
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3 <macros> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
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4 <import>macros.xml</import> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
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5 </macros> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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6 <expand macro="requirements" /> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
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7 <command detect_errors="exit_code"><![CDATA[ |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
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8 #for $counter, $input in enumerate($control): |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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9 ln -s '$input' $input.element_identifier && |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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10 echo ./$new_name >> control && |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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11 #end for |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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12 |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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13 #for $counter, $input in enumerate($conditions): |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
changeset
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14 ln -s '$input' $input.element_identifier && |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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15 echo ./$new_name >> conditions && |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
changeset
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16 #end for |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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17 |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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18 tradis_comparison.R |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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19 --controls control |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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changeset
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20 --conditions conditions |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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21 -o output.csv |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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22 -p plot.pdf |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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23 #if str($filter.filter_selector)=="yes": |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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24 -f |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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25 -t $filter.cutoff |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
changeset
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26 #end if |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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27 ]]> </command> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
changeset
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28 <inputs> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
changeset
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29 <param name="control" type="data" format="csv" multiple="true" label="Control list"/> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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30 <param name="conditions" type="data" format="csv" multiple="true" label="Condition list"/> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
changeset
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31 <conditional name="filter"> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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32 <param name="filter_selector" type="select" label="Filter"> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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33 <option value="yes">Yes</option> |
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09c1f97a5bcc
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
thanhlv
parents:
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34 <option value="no" selected="true">No</option> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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35 </param> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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36 <when value="yes"> |
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09c1f97a5bcc
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
thanhlv
parents:
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diff
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37 <param name="cutoff" type="integer" min="0" value="0" label="Cut-off value"/> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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38 </when> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
diff
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39 <when value="no"/> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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40 </conditional> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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41 |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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42 </inputs> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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43 |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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44 <outputs> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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45 <data name="output" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output.csv"/> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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46 <data name="plot" format="pdf" label="${tool.name} on ${on_string} Plot" from_work_dir="plot.pdf" /> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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47 </outputs> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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48 |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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49 <tests> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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50 <test> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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51 </test> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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52 </tests> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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53 <help><![CDATA[ |
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09c1f97a5bcc
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
thanhlv
parents:
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54 Compares two experimental conditions using the method of Dembek et al. |
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09c1f97a5bcc
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
thanhlv
parents:
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55 mBio 2015. Read counts per gene are compared using edgeR. This analysis |
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09c1f97a5bcc
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
thanhlv
parents:
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56 requires experimental replicates. |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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57 ]]> </help> |
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09c1f97a5bcc
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
thanhlv
parents:
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58 <expand macro="citations" /> |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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59 |
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5506c4307812
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
thanhlv
parents:
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60 </tool> |