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annotate macros.xml @ 0:7d8cafa4d18c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
author iuc
date Sat, 13 May 2023 12:31:25 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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1
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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2 <macros>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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3 <!-- The documentation says a v1.0 is in the works
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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4 but the repository has seen no changes for 3-4 years -->
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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5 <token name="@VERSION@">0.17.17</token>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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6 <token name="@SAMTOOLS_OPTS@"><![CDATA[
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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7 --samtools-threads \${GALAXY_SLOTS:-1}
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8 --samtools-memory \${GALAXY_MEMORY_MB:-100}
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9 ]]></token>
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10 <token name="@LOOMOUT@"><![CDATA[
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11 -o "."
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12 -e "output"
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13 ]]></token>
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14
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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15 <xml name="bcffile" >
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16 <param argument="-b" type="data" format="tabular,txt" optional="true"
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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17 label="Barcodes file to filter BAM"
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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18 help="If -bcfile is not specified the file will be searched in the default position outputted by 'dropest_bc_correct'. Otherwise an error will be thrown" />
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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19 </xml>
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20 <xml name="loomdtype" token_16_selected="true" token_32_selected="false" >
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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21 <param argument="-t" type="select" optional="true"
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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22 label="Datatype of Loom layers"
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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23 help="The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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24 to avoid truncation" >
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25 <option value="uint16" selected="@16_SELECTED@">uint16</option>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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26 <option value="uint32" selected="@32_SELECTED@">uint32</option>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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27 </param>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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28 </xml>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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29 <xml name="repmask" >
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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30 <param argument="-m" type="data" format="gtf" optional="true"
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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31 label="Intervals to mask" />
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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32 </xml>
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
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33 <xml name="notuniquemappings" >
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34 <param argument="-M" type="boolean" truevalue="-M" falsevalue="" checked="false"
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35 label="Consider not unique mappings?" help="(not recommended)" />
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36 </xml>
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37 <xml name="citations">
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38 <citations>
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39 <citation type="doi">10.1038/s41586-018-0414-6</citation>
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40 </citations>
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41 </xml>
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42 <xml name="edam">
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43 <edam_topics>
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44 <edam_topic>topic_3512</edam_topic>
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45 <edam_topic>topic_3320</edam_topic>
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46 </edam_topics>
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47 <edam_operations>
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48 <edam_operation>operation_3800</edam_operation>
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49 </edam_operations>
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50 </xml>
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51 <xml name="requirements">
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52 <requirements>
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53 <requirement type="package" version="@VERSION@" >velocyto.py</requirement>
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54 </requirements>
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55 </xml>
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56 </macros>