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annotate macros.xml @ 1:9655af207032 draft

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 4eb8ee330c85b8b2c157c625247c7b3c8e597fcc
author lldelisle
date Wed, 06 Sep 2023 10:26:13 +0000
parents 8f71aaf6e59d
children 8f9fe0667b89
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8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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1 <macros>
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9655af207032 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 4eb8ee330c85b8b2c157c625247c7b3c8e597fcc
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2 <token name="@VERSION@">0.9.2</token>
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8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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3 <xml name="requirements">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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4 <requirements>
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9655af207032 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 4eb8ee330c85b8b2c157c625247c7b3c8e597fcc
lldelisle
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5 <requirement type="package" version="1.18">htslib</requirement>
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8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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6 <requirement type="package" version="@VERSION@">cooler</requirement>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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7 </requirements>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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8 </xml>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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9 <xml name="stdio">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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10 <stdio>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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11 <!-- Anything other than zero is an error -->
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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12 <exit_code range="1:" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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13 <exit_code range=":-1" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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14 <!-- In case the return code has not been set propery check stderr too -->
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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15 <regex match="Error:" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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16 <regex match="Exception:" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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17 </stdio>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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18 <version_command>cooler --version</version_command>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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19 </xml>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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20 <xml name="size_macro">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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21 <conditional name="size_source">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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22 <param name="size_source_selector" type="select" label="Choose the source for the chromosome sizes">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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23 <option value="cached">Locally cached</option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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24 <option value="history">History</option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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25 </param>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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26 <when value="cached">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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27 <param name="fasta_cached" type="select" label="Fasta availables">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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28 <options from_data_table="fasta_indexes">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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29 <validator type="no_options" message="No cached fasta is available"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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30 </options>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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31 </param>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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32 </when>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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33 <when value="history">
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34 <param name="chromosomeSize" multiple="false" type="data" format="tabular" label="Select a file with the size of chromosome (One column with the chromosome names in the desired order, one column with the sizes)."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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35 </when>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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36 </conditional>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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37 </xml>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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38 <xml name="citation_cooler">
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39 <citations>
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40 <citation type="doi">10.1093/bioinformatics/btz540</citation>
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41 </citations>
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42 </xml>
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43 </macros>