Mercurial > repos > devteam > cufflinks
annotate cuff_macros.xml @ 13:6926716bbfb5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
author | iuc |
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date | Sat, 05 Oct 2024 11:16:09 +0000 |
parents | d080005cffe1 |
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rev | line source |
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7 | 1 <macros> |
13
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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2 <token name="@TOOL_VERSION@">2.2.1</token> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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3 <token name="@PROFILE@">23.1</token> |
10
83bec71c5c9f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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4 |
13
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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5 <xml name="requirements"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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6 <requirements> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">cufflinks</requirement> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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8 <yield /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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9 </requirements> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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10 </xml> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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11 |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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12 <xml name="conditions_repeat" token_format=""> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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13 <repeat name="conditions" title="Condition" min="2"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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14 <param name="name" label="Condition name" type="text"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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15 <validator type="empty_field" message="You must provide a condition name" /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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16 <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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17 </param> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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18 <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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19 </repeat> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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20 </xml> |
10
83bec71c5c9f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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21 |
13
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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22 <xml name="condition_inputs"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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23 <!-- DEFAULT : use BAM/SAM files --> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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24 <conditional name="in_type"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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25 <param name="set_in_type" type="select" label="Input data type" |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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26 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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27 <option value="BAM">SAM/BAM</option> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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28 <option value="CXB">Cuffquant (CXB)</option> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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29 <option value="CONDITION_LIST">List of single replicate conditions</option> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
parents:
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30 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
parents:
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31 </param> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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32 <when value="BAM"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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33 <expand macro="conditions_repeat" format="sam,bam" /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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34 </when> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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35 <when value="CXB"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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36 <expand macro="conditions_repeat" format="cxb" /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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37 </when> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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38 <when value="CONDITION_LIST"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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39 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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40 </when> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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41 <when value="CONDITION_REPLICATE_LIST"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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43 </when> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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44 </conditional> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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45 </xml> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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46 <token name="@CONDITION_SAMPLES@"><![CDATA[ |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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47 #if $in_type.set_in_type in ['BAM', 'CXB'] |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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48 #for $condition in $in_type.conditions: |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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49 #set samples = ','.join([str($sample) for $sample in $condition.samples]) |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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50 '$samples' |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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51 #end for |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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52 #elif $in_type.set_in_type == 'CONDITION_LIST' |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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53 #for $sample in $in_type.conditions: |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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54 '$sample' |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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55 #end for |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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56 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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57 #for $condition_list in $in_type.conditions: |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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58 #set samples = ','.join([str($sample) for $sample in $condition_list]) |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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59 '$samples' |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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60 #end for |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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61 #end if |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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62 ]]></token> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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63 <token name="@CONDITION_LABELS@"><![CDATA[ |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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64 #import re |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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65 #if $in_type.set_in_type in ['BAM', 'CXB'] |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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66 #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions]) |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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67 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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68 #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()]) |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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69 #end if |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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70 --labels '$labels' |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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71 ]]></token> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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72 <xml name="cufflinks_gtf_inputs"> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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73 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
iuc
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74 </xml> |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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75 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[ |
6926716bbfb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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76 ## Inputs. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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77 #for $i, $input_file in enumerate($inputs): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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78 ln -s '${input_file}' input_$i && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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79 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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80 ]]></token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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81 <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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82 ## Inputs. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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83 #for $i, $input_file in enumerate($inputs): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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84 'input_$i' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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85 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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86 ]]></token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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87 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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88 |
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89 <xml name="citations"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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90 <citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
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91 <citation type="doi">10.1038/nbt.1621</citation> |
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92 <yield/> |
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93 </citations> |
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94 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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95 |
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96 </macros> |