Mercurial > repos > iuc > crossmap_wig
annotate crossmap_wig.xml @ 6:5f893ed3c5ed draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ce9efed8c15240a269107ff356aeb18b52eb383f"
author | iuc |
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date | Wed, 30 Sep 2020 14:01:51 +0000 |
parents | 8c26026e7ad9 |
children | 282a658c6569 |
rev | line source |
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3
8c26026e7ad9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
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1 <tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@"> |
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0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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3 <macros> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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4 <import>macros.xml</import> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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5 </macros> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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6 <expand macro="requirements"/> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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7 <expand macro="stdio"/> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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8 <expand macro="version_command"/> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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9 <command><![CDATA[ |
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81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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10 CrossMap.py wig |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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11 '${chain_source.input_chain}' |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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12 '${input}' |
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8c26026e7ad9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
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13 output |
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0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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14 ]]></command> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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15 |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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16 <inputs> |
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81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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17 <param name="input" type="data" format="wig" label="Wiggle file"/> |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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18 |
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0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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19 <expand macro="chain" /> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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changeset
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20 </inputs> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
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21 |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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22 <outputs> |
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8c26026e7ad9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
parents:
2
diff
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23 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" /> |
8c26026e7ad9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
parents:
2
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24 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" /> |
0
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
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25 </outputs> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
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26 |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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27 <tests> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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28 <!-- WIG - Doesn't understand fixedStep --> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
changeset
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29 <test> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
changeset
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30 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> |
1
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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31 <param name="index_source" value="history"/> |
0
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
changeset
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32 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
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33 |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
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34 <output name="output" file="test_wig_01_output_a.bw"/> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
changeset
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35 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff
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36 </test> |
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81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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37 |
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d0e7cc22351f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
iuc
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38 <test><!-- cached reference genome --> |
d0e7cc22351f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
iuc
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39 <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" /> |
1
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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40 <param name="index_source" value="cached"/> |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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41 |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
0
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42 <output name="output" file="test_wig_01_output_a.bw"/> |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
0
diff
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43 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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44 </test> |
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0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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45 </tests> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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46 <help><![CDATA[ |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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47 @HELP_GENERAL@ |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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48 |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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49 Wig |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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50 --- |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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51 |
1
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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52 Input wiggle data can be in variableStep (for data with irregular |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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53 intervals) or fixedStep (for data with regular intervals). Regardless of |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
0
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54 the input, the output will always in bedGraph format. bedGraph format is |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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55 similar to wiggle format and can be converted into BigWig format using UCSC |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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56 wigToBigWig tool. We export files in bedGraph because it is usually much |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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0
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57 smaller than file in wiggle format, and more importantly, CrossMap |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
0
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58 internally transforms wiggle into bedGraph to increase running speed. |
81986a56b281
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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59 ]]></help> |
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0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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60 |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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61 <citations> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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62 <citation type="doi">10.1093/bioinformatics/btt730</citation> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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63 </citations> |
0e6f675cea09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
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64 </tool> |