Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
annotate readmap.xml @ 8:be0c6b6466cc draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
author | mvdbeek |
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date | Mon, 19 Sep 2016 06:16:21 -0400 |
parents | 68f58363f1c6 |
children | 92898cc3ea19 |
rev | line source |
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8
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.0"> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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changeset
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2 <description>from sRbowtie aligment</description> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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3 <requirements> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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diff
changeset
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4 <requirement type="package" version="1.0.0">bowtie</requirement> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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5 <requirement type="package" version="0.9.0">pysam</requirement> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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diff
changeset
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6 <requirement type="package" version="1.9.3">numpy</requirement> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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7 <requirement type="package" version="1.3.0">r-optparse</requirement> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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8 <requirement type="package" version="0.6_26">r-latticeextra</requirement> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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9 <requirement type="package" version="2.0.0">r-gridextra</requirement> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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10 </requirements> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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11 <command><![CDATA[ |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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12 python2 $__tool_directory__/readmap.py |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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13 #if $refGenomeSource.genomeSource == "history": |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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14 --reference_fasta |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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15 $refGenomeSource.ownFile ## index source |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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changeset
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16 #else: |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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17 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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changeset
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18 --reference_bowtie_index |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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19 $reference |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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20 #end if |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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changeset
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21 --output_readmap |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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22 "$readmap_dataframe" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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23 --output_size_distribution |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
diff
changeset
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24 "$size_distribution_dataframe" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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25 --minquery $minquery |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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26 --maxquery $maxquery |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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27 --input |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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28 #for $i in $refGenomeSource.series |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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29 $i.input |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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30 #end for |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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31 --ext |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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32 #for $i in $refGenomeSource.series |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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33 $i.input.ext |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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34 #end for |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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35 --label |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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36 #for $i in $refGenomeSource.series |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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37 "$i.input.name" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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38 #end for |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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39 --normalization_factor |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
6
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40 #for $i in $refGenomeSource.series |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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41 $i.norm |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
parents:
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42 #end for |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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43 #if $gff: |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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44 --gff |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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45 $gff |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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46 #end if |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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47 ; Rscript $__tool_directory__/plot_size_readmap.r |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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48 --readmap_tab "$readmap_dataframe" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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49 --size_distribution_tab "$size_distribution_dataframe" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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50 --readmap_pdf "$readmap_PDF" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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51 --size_distribution_pdf "$size_PDF" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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52 --combi_pdf "$combi_PDF" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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53 --title "$title" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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54 --xlabel "$xlabel" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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55 --ylabel "$ylabel" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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56 --yrange "$yrange" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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57 --rows_per_page "$rows_per_page" |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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58 ]]> |
0
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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59 </command> |
8
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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60 <inputs> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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61 <conditional name="refGenomeSource"> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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62 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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63 <option value="indexed">Use a built-in index</option> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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64 <option value="history">Use one from the history</option> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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65 </param> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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66 <when value="indexed"> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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67 <repeat name="series" title="Add alignment files"> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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68 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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69 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> |
be0c6b6466cc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
mvdbeek
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70 </param> |
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71 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> |
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72 </repeat> |
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73 </when> |
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74 <when value="history"> |
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75 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" /> |
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76 <repeat name="series" title="Add alignment files"> |
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77 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> |
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78 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> |
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79 </repeat> |
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80 </when> |
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81 </conditional> |
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82 <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> |
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83 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> |
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84 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/> |
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85 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/> |
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86 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/> |
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87 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/> |
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88 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> |
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89 <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/> |
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90 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> |
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91 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> |
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92 </param> |
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93 </inputs> |
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94 <outputs> |
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95 <data format="tabular" name="readmap_dataframe" label="Readmap dataframe"/> |
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96 <data format="tabular" name="size_distribution_dataframe" label="Size distribution dataframe"/> |
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97 <data format="pdf" name="readmap_PDF" label="Readmaps"/> |
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98 <data format="pdf" name="size_PDF" label="Size distribution"/> |
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99 <data format="pdf" name="combi_PDF" label="Size distribution and Readmaps"/> |
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100 </outputs> |
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101 <help> |
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102 |
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103 **What it does** |
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104 |
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105 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a "Readmap", |
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106 where by default for each "chromosome" the position of the read is recorded on the x-axis, and the y-axis indicates |
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107 the number of reads per position. Reads that map in sense are on the top, reads that map antisense are on the bottom. |
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108 |
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109 |
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110 .. class:: warningmark |
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111 |
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112 '''TIP''' The input data can be produced using the sRbowtie tool. |
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113 |
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114 ---- |
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115 |
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116 '''Example''' |
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117 |
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118 Query sequence:: |
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119 For a SAM file as the following: |
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120 |
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121 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0 |
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122 |
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123 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0 |
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124 |
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125 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0 |
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126 |
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127 produce a plot like this: |
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128 |
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129 ---- |
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130 |
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131 .. image:: static/images/readmap.png |
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132 :height: 800 |
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133 :width: 500 |
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134 |
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135 </help> |
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136 <tests> |
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137 <test> |
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138 <param name="genomeSource" value="history" /> |
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139 <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> |
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140 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/> |
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141 <param name="series_0|norm" value="1" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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142 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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143 <param name="series_1|norm" value="1" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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144 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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145 <param name="series_2|norm" value="1" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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146 <param name="minquery" value="20" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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147 <param name="maxquery" value="30" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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148 <param name="title" value="Readmaps and size distributions" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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149 <param name="xlabel" value="Coordinates/read size" /> |
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150 <param name="ylabel" value="Number of reads" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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151 <param name="rows_per_page" value="8" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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152 <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" /> |
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153 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" /> |
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154 </test> |
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155 </tests> |
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156 </tool> |