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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit ef98cc8b7da02cdbc685b17ee9a041b6f0bc7636
author bgruening
date Mon, 03 Mar 2025 10:25:39 +0000
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2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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1 <tool id="hictk" name="hictk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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2 <description>convert cool to juicebox hic</description>
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3 <macros>
3
1b5c5779eff2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit ef98cc8b7da02cdbc685b17ee9a041b6f0bc7636
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4 <token name="@TOOL_VERSION@">2.0.2</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement version="@TOOL_VERSION@" type="package">hictk</requirement>
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9 </requirements>
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10 <version_command><![CDATA[echo "@TOOL_VERSION@"]]></version_command>
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11 <command><![CDATA[
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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12 hictk convert -f --output-fmt 'hic' '$incool' '$outhic'
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13 ]]></command>
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14 <inputs>
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15 <param name="incool" type="data" format="cool,mcool,scool" label="cool/hdf5 data to convert to hic binary" />
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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16 </inputs>
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17 <outputs>
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18 <data name="outhic" format="juicebox_hic" label="hictk convert on $incool.element_identifier hic" hidden="false"/>
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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19 </outputs>
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20 <tests>
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21 <test>
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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22 <param name="incool" value="incool_sample"/>
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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23 <output name="outhic" value="outhic_sample" compare="sim_size" delta_frac="0.1" ftype="juicebox_hic" />
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24 </test>
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25 </tests>
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26 <help><![CDATA[
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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27 This tool converts cool/mcool/scool format files into hic binary files
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28
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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29 **hictk**
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30
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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31 hictk is a blazing fast toolkit to work with .hic and .cool files.
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32
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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33 This repository hosts `hictk`: a set of CLI tools to work with Cooler, as well as `libhictk`: the C++ library underlying `hictk`.
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34
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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35 hictk_ is capable of reading files in `.cool`, `.mcool`, `.scool` and `.juicebox_hic` format (including hic v9) as well as writing `.cool` and `.mcool` files
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36 but this tool only writes `juicebox_hic` at present.
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37
2ca594a0caf7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hictk commit 54016bc79390196fa61e89081f629b2c13fc6f1e
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38 .. _hictk: https://github.com/paulsengroup/hictk
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39
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40 ]]></help>
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41 <citations>
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42 <citation type="bibtex">@article{hictk,
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43 author = {Roberto Rossini},
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44 year = {2023},
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45 url = {https://github.com/paulsengroup/hictk},
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46 title = {hictk: blazing fast toolkit to work with .hic and .cool files}
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47 }</citation>
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48 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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49 </citations>
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50 </tool>