Mercurial > repos > iuc > velocyto_cli
comparison macros.xml @ 0:7d8cafa4d18c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
author | iuc |
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date | Sat, 13 May 2023 12:31:25 +0000 |
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-1:000000000000 | 0:7d8cafa4d18c |
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1 | |
2 <macros> | |
3 <!-- The documentation says a v1.0 is in the works | |
4 but the repository has seen no changes for 3-4 years --> | |
5 <token name="@VERSION@">0.17.17</token> | |
6 <token name="@SAMTOOLS_OPTS@"><![CDATA[ | |
7 --samtools-threads \${GALAXY_SLOTS:-1} | |
8 --samtools-memory \${GALAXY_MEMORY_MB:-100} | |
9 ]]></token> | |
10 <token name="@LOOMOUT@"><![CDATA[ | |
11 -o "." | |
12 -e "output" | |
13 ]]></token> | |
14 | |
15 <xml name="bcffile" > | |
16 <param argument="-b" type="data" format="tabular,txt" optional="true" | |
17 label="Barcodes file to filter BAM" | |
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" /> | |
19 </xml> | |
20 <xml name="loomdtype" token_16_selected="true" token_32_selected="false" > | |
21 <param argument="-t" type="select" optional="true" | |
22 label="Datatype of Loom layers" | |
23 help="The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32 | |
24 to avoid truncation" > | |
25 <option value="uint16" selected="@16_SELECTED@">uint16</option> | |
26 <option value="uint32" selected="@32_SELECTED@">uint32</option> | |
27 </param> | |
28 </xml> | |
29 <xml name="repmask" > | |
30 <param argument="-m" type="data" format="gtf" optional="true" | |
31 label="Intervals to mask" /> | |
32 </xml> | |
33 <xml name="notuniquemappings" > | |
34 <param argument="-M" type="boolean" truevalue="-M" falsevalue="" checked="false" | |
35 label="Consider not unique mappings?" help="(not recommended)" /> | |
36 </xml> | |
37 <xml name="citations"> | |
38 <citations> | |
39 <citation type="doi">10.1038/s41586-018-0414-6</citation> | |
40 </citations> | |
41 </xml> | |
42 <xml name="edam"> | |
43 <edam_topics> | |
44 <edam_topic>topic_3512</edam_topic> | |
45 <edam_topic>topic_3320</edam_topic> | |
46 </edam_topics> | |
47 <edam_operations> | |
48 <edam_operation>operation_3800</edam_operation> | |
49 </edam_operations> | |
50 </xml> | |
51 <xml name="requirements"> | |
52 <requirements> | |
53 <requirement type="package" version="@VERSION@" >velocyto.py</requirement> | |
54 </requirements> | |
55 </xml> | |
56 </macros> |