Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff
annotate filter-below-abund.xml @ 10:00f7064c564b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author | iuc |
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date | Thu, 03 Oct 2024 13:46:21 +0000 |
parents | 19607c740d19 |
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rev | line source |
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8
b469ab47b490
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
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1 <tool id="khmer_filter_below_abundance_cutoff" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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2 <description> |
1
e0e33e40d7c4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
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3 below k-mer abundance of 50 |
0
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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4 </description> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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changeset
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5 <macros> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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changeset
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6 <token name="@BINARY@">filter-below-abund.py</token> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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7 <import>macros.xml</import> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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8 </macros> |
10
00f7064c564b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents:
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9 <expand macro="bio_tools"/> |
7
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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10 <expand macro="requirements"> |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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11 <requirement type="package" version="1.0.1">screed</requirement> |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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12 </expand> |
0
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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13 <expand macro="stdio" /> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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14 <command><![CDATA[ |
7
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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15 @LINK_SEQUENCES@ |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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16 mkdir output && |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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17 cd output && |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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18 python '$__tool_directory__/@BINARY@' |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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19 '${input_countgraph_filename}' |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
6
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20 @USE_SEQUENCES@ |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
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21 ]]> |
0
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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22 </command> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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23 <inputs> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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24 <expand macro="input_sequences_filenames" /> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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25 <expand macro="input_countgraph_filename" /> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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26 </inputs> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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27 <outputs> |
7
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
6
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28 <expand macro="output_sequences" extension="below"/> |
0
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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29 </outputs> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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30 <tests> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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31 <test> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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32 <param name="inputs" value="test-abund-read-2.fa" /> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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33 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" /> |
7
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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34 <output_collection name="sequences"> |
569001af897d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
6
diff
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35 <element name="test-abund-read-2.fa" file="test-abund-read-2.fa.below" /> |
0
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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36 </output_collection> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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37 </test> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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38 </tests> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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39 <help><![CDATA[ |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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40 Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph. |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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41 |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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42 @HELP_FOOTER@ |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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43 ]]></help> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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44 <citations> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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45 <expand macro="software-citation" /> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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46 <expand macro="counting-citation" /> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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47 </citations> |
67b597ec0baf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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48 </tool> |