Mercurial > repos > iuc > humann2_join_tables

annotate humann2_join_tables.xml @ 7:d05ac93eabf3 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 06:59:42 +0000
parents 300fd72ce167
children
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300fd72ce167 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
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1 <tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.2">
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14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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2 <description>HUMAnN2 generated tables</description>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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3 <macros>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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4 <import>humann2_macros.xml</import>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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5 </macros>
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300fd72ce167 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
parents: 4
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6 <expand macro="stdio"/>
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14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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7 <expand macro="requirements"/>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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8 <expand macro="version"/>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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9 <command detect_errors="exit_code"><![CDATA[
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9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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10 mkdir tmp_dir
9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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11 &&
9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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12 #for $table in $input_table
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12103efd0e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit f24d561fc65cc7204e53a6a65014130aaa65aa57"
iuc
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13 #set orig_filename=$table.element_identifier
12103efd0e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit f24d561fc65cc7204e53a6a65014130aaa65aa57"
iuc
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14 #set new_filename='_'.join($orig_filename.split(' '))
12103efd0e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit f24d561fc65cc7204e53a6a65014130aaa65aa57"
iuc
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15 cp '$table' 'tmp_dir/$new_filename' &&
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9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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16 #end for
9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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17 humann2_join_tables
9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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18 -i 'tmp_dir'
9ada8e95bdd0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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19 -o '$joined_table'
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14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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20 ]]></command>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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21 <inputs>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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22 <param name="input_table" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/>
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23 </inputs>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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24 <outputs>
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25 <data format="tsv" name="joined_table" label="${tool.name} on ${on_string}: Joined table" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input_table" value="demo_pathabundance.tsv,demo_pathcoverage.tsv"/>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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30 <output name="joined_table">
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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31 <assert_contents>
14d5bf0d63a0 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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32 <has_text text="PWY490-3: nitrate reduction VI (assimilatory)|unclassified" />
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33 <has_text text="PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I" />
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34 <has_text text="VALSYN-PWY: L-valine biosynthesis" />
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35 <has_text text="UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 @HELP_HEADER@
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42
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43 Join HUMAnN2 tables is a tool to join gene or pathway tables of multiple samples into a single table.
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44 ]]></help>
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45 <expand macro="citations"/>
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46 </tool>