Mercurial > repos > artbio > small_rna_maps
annotate small_rna_maps.xml @ 10:c3fb2a864526 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6eb3992d56ee12b901b278f2a07bed719c5d0675
author | artbio |
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date | Tue, 07 Nov 2017 17:38:39 -0500 |
parents | 3ea75c573429 |
children | a561a71bd7d7 |
rev | line source |
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10
c3fb2a864526
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6eb3992d56ee12b901b278f2a07bed719c5d0675
artbio
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.4.1"> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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2 <description></description> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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3 <requirements> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement> |
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a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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9 <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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10 |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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11 </requirements> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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12 <stdio> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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13 <exit_code range="1:" level="fatal" description="Tool exception" /> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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14 </stdio> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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15 <command detect_errors="exit_code"><![CDATA[ |
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507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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16 #for $file in $inputs |
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6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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17 samtools index '$file' && |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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18 #end for |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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19 python '$__tool_directory__'/small_rna_maps.py |
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507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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20 --inputs |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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21 #for $file in $inputs |
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6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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22 '$file' |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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23 #end for |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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24 --sample_names |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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changeset
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25 #for $sample in $inputs |
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6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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26 '$sample.name' |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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27 #end for |
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1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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28 --minsize $minsize |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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29 --maxsize $maxsize |
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3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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30 --cluster $cluster |
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12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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31 #if str($plots_options.plots_options_selector ) == "two_plot": |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' |
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ed8b0142538d
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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33 --outputs '$output_tab' '$extra_output_tab' && |
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a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
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34 #elif str($plots_options.plots_options_selector ) == "global": |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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35 --plot_methods 'Size' |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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36 --outputs '$output_tab' && |
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12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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37 #else: |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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38 --plot_methods '${plots_options.first_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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39 --outputs '$output_tab' && |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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40 #end if |
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507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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41 Rscript '$__tool_directory__'/small_rna_maps.r |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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42 --first_dataframe '$output_tab' |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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43 --extra_dataframe '$extra_output_tab' |
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a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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44 --normalization '$normalization' |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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45 #if str($plots_options.plots_options_selector ) == "two_plot": |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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46 --first_plot_method '${plots_options.first_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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47 --extra_plot_method '${plots_options.extra_plot}' |
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a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
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48 #elif str($plots_options.plots_options_selector ) == "global": |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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49 --first_plot_method 'Size' |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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50 --extra_plot_method '' |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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51 --global '${plots_options.mergestrands}' |
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12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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52 #else: |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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53 --first_plot_method '${plots_options.first_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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54 --extra_plot_method '' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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55 #end if |
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a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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56 --output_pdf '$output_pdf' |
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6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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57 ]]></command> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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58 <inputs> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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59 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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60 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)" |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
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61 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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62 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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63 value="0" help="default value: 0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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64 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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65 value="10000" help="default value: 10000" /> |
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3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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66 <param name="cluster" type="integer" label="aggregation distance in nucleotides" |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
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67 value="0" help="if not 0, sets the distance (in nt) below which data are clustered to a single median position" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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68 <conditional name="plots_options"> |
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a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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69 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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70 <option value="one_plot">Just one plot per chromosome</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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71 <option value="two_plot" selected="True">Two plots per chromosome</option> |
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a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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72 <option value="global">Global read size distributions of aligned reads</option> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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73 </param> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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74 <when value="two_plot"> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
75 <param name="first_plot" type="select" display="radio" label="Select the type of the first plot"> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
76 <option value="Counts">Counts</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
77 <option value="Coverage">Coverage</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
78 <option value="Mean">Mean Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
79 <option value="Median">Median Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
80 <option value="Size">Size Distributions</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
81 </param> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
82 <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot"> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
83 <option value="Counts">Counts</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
84 <option value="Coverage">Coverage</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
85 <option value="Mean">Mean Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
86 <option value="Median">Median Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
87 <option value="Size">Size Distributions</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
88 </param> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
89 </when> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
90 <when value="one_plot"> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
91 <param name="first_plot" type="select" display="radio" label="select the type of the first plot"> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
92 <option value="Counts">Counts</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
93 <option value="Coverage">Coverage</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
94 <option value="Mean">Mean Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
95 <option value="Median">Median Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
96 <option value="Size">Size Distributions</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
97 </param> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
98 </when> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
99 <when value="global"> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
100 <param name="first_plot" type="hidden" value="Size"/> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
101 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram"> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
102 <option value="nomerge">Do not merge</option> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
103 <option value="merge">Merge forward and reverse reads</option> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
104 </param> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
105 </when> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
106 </conditional> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
107 </inputs> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
108 |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
109 <outputs> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
110 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
111 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe"> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
112 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
113 </data> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
114 <data format="pdf" name="output_pdf" label="small RNA maps" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
115 </outputs> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
116 |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
117 <tests> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
118 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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120 <param name="minsize" value="0" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
121 <param name="cluster" value="5" /> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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122 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
123 <param name="plots_options_selector" value="one_plot" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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124 <param name="normalization" value="1 1" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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125 <param name="first_plot" value="Counts" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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126 <output file="count_cluster_5.tab" name="output_tab" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
127 <output file="count_cluster_5.pdf" name="output_pdf" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
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changeset
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128 </test> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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129 <test> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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130 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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131 <param name="minsize" value="0" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
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changeset
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132 <param name="maxsize" value="10000" /> |
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
133 <param name="cluster" value="0" /> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
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134 <param name="plots_options_selector" value="global" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
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135 <param name="mergestrands" value="nomerge" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
136 <param name="first_plot" value="Size" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
137 <param name="normalization" value="1 1" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
138 <output file="size.tab" name="output_tab" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
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139 <output file="global_nomerge.pdf" name="output_pdf" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
140 </test> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
141 <test> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
142 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
143 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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144 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
145 <param name="cluster" value="0" /> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
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146 <param name="plots_options_selector" value="global" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
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147 <param name="mergestrands" value="merge" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
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148 <param name="first_plot" value="Size" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
149 <param name="normalization" value="1 1" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
150 <output file="size.tab" name="output_tab" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
151 <output file="global_merge.pdf" name="output_pdf" /> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
152 </test> |
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
153 <test> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
154 <param name="inputs" value="input1.bam" ftype="bam"/> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
155 <param name="minsize" value="20" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
156 <param name="maxsize" value="30" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
157 <param name="cluster" value="0" /> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
158 <param name="plots_options_selector" value="global" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
159 <param name="mergestrands" value="merge" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
160 <param name="first_plot" value="Size" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
161 <param name="normalization" value="1 1" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
162 <output file="size20-30.tab" name="output_tab" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
163 <output file="global_merge_20-30.pdf" name="output_pdf" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
164 </test> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
165 <test> |
7
a96e6a7df2b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents:
6
diff
changeset
|
166 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
167 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
168 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
169 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
170 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
171 <param name="first_plot" value="Counts" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
172 <param name="extra_plot" value="Mean" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
173 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
174 <output file="count.tab" name="output_tab" /> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
175 <output file="mean.tab" name="extra_output_tab" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
176 <output file="count-mean.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
177 </test> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
178 <test> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
179 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
180 <param name="minsize" value="20" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
181 <param name="maxsize" value="30" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
182 <param name="cluster" value="0" /> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
183 <param name="plots_options_selector" value="two_plot" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
184 <param name="first_plot" value="Counts" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
185 <param name="extra_plot" value="Mean" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
186 <param name="normalization" value="1 1" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
187 <output file="count20-30.tab" name="output_tab" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
188 <output file="mean20-30.tab" name="extra_output_tab" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
189 <output file="count-mean-20-30.pdf" name="output_pdf" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
190 </test> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
191 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
192 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
193 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
194 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
195 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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196 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
197 <param name="first_plot" value="Counts" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
198 <param name="extra_plot" value="Mean" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
199 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
200 <output file="doubled_count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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201 <output file="doubled_mean.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
202 <output file="doubled_count-mean.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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203 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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204 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
205 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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206 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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207 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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208 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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209 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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210 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
211 <param name="extra_plot" value="Median" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
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212 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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213 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
214 <output file="median.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
215 <output file="count-median.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
216 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
217 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
218 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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219 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
220 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
221 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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222 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
223 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
224 <param name="extra_plot" value="Coverage" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
225 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
226 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
227 <output file="coverage.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
228 <output file="count-coverage.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
229 </test> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
230 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
231 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
232 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
233 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
234 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
235 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
236 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
237 <param name="extra_plot" value="Size" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
238 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
239 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
240 <output file="size.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
241 <output file="count-size.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
242 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
243 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
244 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
245 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
246 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
247 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
248 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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249 <param name="first_plot" value="Size" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
250 <param name="extra_plot" value="Counts" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
251 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
252 <output file="size.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
253 <output file="count.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
254 <output file="size-count.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
255 </test> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
256 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
257 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
258 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
|
259 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
260 <param name="cluster" value="0" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
261 <param name="plots_options_selector" value="two_plot" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
262 <param name="first_plot" value="Size" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
263 <param name="extra_plot" value="Counts" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
264 <param name="normalization" value="1 0.75" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
265 <output file="size.tab" name="output_tab" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
266 <output file="count.tab" name="extra_output_tab" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
267 <output file="size-count_normed.pdf" name="output_pdf" /> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
268 </test> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
269 <test> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
270 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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271 <param name="minsize" value="0" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
|
272 <param name="cluster" value="0" /> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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273 <param name="maxsize" value="10000" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
274 <param name="plots_options_selector" value="one_plot" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
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275 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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276 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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277 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
278 <output file="count.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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279 </test> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
280 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
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281 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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282 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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283 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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284 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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285 <param name="plots_options_selector" value="one_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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286 <param name="first_plot" value="Size" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
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287 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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288 <output file="size.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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289 <output file="size.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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290 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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291 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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292 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
8
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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293 <param name="minsize" value="0" /> |
1827b74f872b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents:
7
diff
changeset
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294 <param name="maxsize" value="10000" /> |
9
3ea75c573429
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents:
8
diff
changeset
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295 <param name="cluster" value="0" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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296 <param name="plots_options_selector" value="one_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
297 <param name="first_plot" value="Coverage" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
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298 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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299 <output file="coverage.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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300 <output file="coverage.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
301 </test> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
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302 <test> |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
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303 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
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304 <param name="minsize" value="0" /> |
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305 <param name="maxsize" value="10000" /> |
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306 <param name="cluster" value="0" /> |
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307 <param name="plots_options_selector" value="one_plot" /> |
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308 <param name="first_plot" value="Coverage" /> |
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309 <param name="normalization" value="1 0.2" /> |
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310 <output file="coverage.tab" name="output_tab" /> |
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311 <output file="coverage_normed.pdf" name="output_pdf" /> |
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312 </test> |
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313 </tests> |
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314 |
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315 |
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316 <help> |
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317 |
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318 **What it does** |
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319 |
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320 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5) |
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321 size read distribution along chromosome references. |
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322 |
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323 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads |
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324 whose 5' end map to a given coordinate in a chromosome reference. |
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325 Coverage depths are computed from the input bam alignment files using the python pysam module. |
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326 |
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327 The variables mentioned above (1-5) can be plotted either separately or in all possible |
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328 pairwise combinations. |
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329 |
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330 For comparison purpose, values from bam alignment files can be normalized by a size factor |
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331 before plotting. If the normalization field is leaved blank, default normalization of 1 |
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332 is assumed. |
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333 |
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334 **Inputs** |
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335 |
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336 bam alignment files that must be |
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337 |
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338 - single-read |
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339 - sorted |
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340 - mapping to the same reference |
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341 |
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342 Optionally, a space-separated list of normalization/size factors may be added before plotting. |
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343 This list maps to the selected bam alignments from bottom to top. |
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344 |
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345 **Output** |
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346 |
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347 A pdf file generated by the R package lattice |
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348 |
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349 One or two dataframes used to plot data |
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350 |
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351 </help> |
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352 |
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353 <citations> |
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354 <citation type="doi">10.1093/bioinformatics/btp352</citation> |
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355 <citation type="bibtex">@Book{, |
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356 title = {Lattice: Multivariate Data Visualization with R}, |
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357 author = {Deepayan Sarkar}, |
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358 publisher = {Springer}, |
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359 address = {New York}, |
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360 year = {2008}, |
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361 note = {ISBN 978-0-387-75968-5}, |
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362 url = {http://lmdvr.r-forge.r-project.org}, |
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363 }</citation> |
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364 </citations> |
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365 </tool> |
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366 |