Mercurial > repos > iuc > rasusa
annotate rasusa.xml @ 3:add156116c63 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
author | iuc |
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date | Wed, 10 Jul 2024 17:01:16 +0000 |
parents | c8f1cd6c1fbf |
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rev | line source |
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0
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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1 <tool id="rasusa" name="rasusa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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2 <description>Randomly subsample reads to a specified coverage</description> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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3 <macros> |
3
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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4 <token name="@TOOL_VERSION@">2.0.0</token> |
0
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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5 <token name="@VERSION_SUFFIX@">0</token> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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6 <token name="@FORMATS@">fastqsanger,fastqsanger.gz,fasta,fasta.gz</token> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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7 <xml name="size_units"> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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8 <option value="b">bases</option> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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9 <option value="k">Kilo bases</option> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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10 <option value="m">Mega bases</option> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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11 <option value="g">Giga bases</option> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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12 <option value="t">Tera bases</option> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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13 </xml> |
3
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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14 <xml name="params_fastq"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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15 <conditional name="subsample"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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16 <param name="type" type="select" label="Subsample reads based on"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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17 <option value="coverage">Coverage</option> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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18 <option value="num_bases">Number of bases</option> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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19 <option value="num_reads">Number of reads</option> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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20 <option value="frac_reads" selected="true">Fraction of reads</option> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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21 </param> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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22 <when value="coverage"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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23 <param name="genome_size_unit" type="select" label="Specify genome size in"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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24 <expand macro="size_units" /> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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25 </param> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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26 <param name="genome_size" type="float" min="0" value="" label="Genome size to calculate coverage with respect to"/> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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27 <param argument="--coverage" type="float" min="0" value="" label="The desired coverage to subsample the reads to"/> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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28 </when> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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29 <when value="num_bases"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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30 <param name="num_bases_unit" type="select" label="Specify number of bases in"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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31 <expand macro="size_units" /> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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32 </param> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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33 <param name="bases" type="float" min="0" value="" label="Explicitly set the number of bases required"/> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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34 </when> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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35 <when value="num_reads"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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36 <param argument="--num" type="integer" value="" min="1"/> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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37 </when> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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38 <when value="frac_reads"> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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39 <param argument="--frac" type="float" value="0.1" min="0" max="1"/> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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40 </when> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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41 </conditional> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
changeset
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42 </xml> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
diff
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43 <token name="@FASTQ_SUBSAMPLE_OPTIONS@"><![CDATA[ |
0
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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44 #if str( $subsample.type ) == "coverage": |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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45 --genome-size '$subsample.genome_size$subsample.genome_size_unit' |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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46 --coverage $subsample.coverage |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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47 #elif str( $subsample.type ) == "num_bases": |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
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48 --bases '$subsample.bases$subsample.num_bases_unit' |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
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49 #elif str( $subsample.type ) == "num_reads": |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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50 --num $subsample.num |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
changeset
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51 #elif str( $subsample.type ) == "frac_reads": |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
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52 --frac $subsample.frac |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
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53 #end if |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
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54 #if $r1_ext.endswith(".gz") or $r2_ext.endswith(".gz") |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
parents:
diff
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55 --output-type g |
3
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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56 #end if ]]> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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57 </token> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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58 </macros> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
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59 <xrefs> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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60 <xref type='bio.tools'>rasusa</xref> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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61 </xrefs> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
2
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62 <requirements> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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63 <requirement type="package" version="@TOOL_VERSION@">rasusa</requirement> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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64 <requirement type="package" version="1.20">samtools</requirement> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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65 </requirements> |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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66 |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
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67 <command detect_errors="exit_code"><![CDATA[ |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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68 #if str( $input.input_selector ) == "aligned": |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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69 ln -s '$bam' 'input.bam' && |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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70 ln -s '$bam.metadata.bam_index' 'input.bam.bai' && |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
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71 rasusa aln |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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72 --coverage $input.coverage |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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73 --step-size $input.step_size |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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74 #else: |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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75 rasusa reads |
0
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
iuc
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76 #end if |
3
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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77 |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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78 #if $seed |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
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79 -s $seed |
add156116c63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
iuc
parents:
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80 #end if |
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81 |
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82 #if str( $input.input_selector ) == "paired": |
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83 #set r1_ext = $input.reads1.extension |
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84 #set r2_ext = $input.reads2.extension |
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85 -o 'paired_out1.$r1_ext' |
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86 -o 'paired_out2.$r2_ext' |
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87 @FASTQ_SUBSAMPLE_OPTIONS@ |
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88 '${input.reads1}' |
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89 '${input.reads2}' && |
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90 mv 'paired_out1.$r1_ext' '$paired_output1' && |
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91 mv 'paired_out2.$r2_ext' '$paired_output2' |
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92 |
0
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93 #elif str( $input.input_selector ) == "paired_collection": |
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94 #set r1_ext = $input.collection.forward.extension |
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95 #set r2_ext = $input.collection.reverse.extension |
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96 -o 'paired_out1.$r1_ext' |
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97 -o 'paired_out2.$r2_ext' |
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98 @FASTQ_SUBSAMPLE_OPTIONS@ |
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99 '${input.collection.forward}' |
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100 '${input.collection.reverse}' && |
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101 mv 'paired_out1.$r1_ext' '${collection_output.forward}' && |
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102 mv 'paired_out2.$r2_ext' '${collection_output.reverse}' |
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103 |
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104 #elif str( $input.input_selector ) == "single": |
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105 #set r1_ext = $input.reads.extension |
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106 -o 'single_out.$r1_ext' |
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107 @FASTQ_SUBSAMPLE_OPTIONS@ |
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108 '${input.reads}' && |
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109 mv 'single_out.$r1_ext' '$single_output' |
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110 |
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111 #elif str( $input.input_selector ) == "aligned": |
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112 'input.bam' | samtools sort --no-PG -@ 1 -T '\${TMPDIR:-.}' -O bam -o '$bam_output' - |
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113 #end if |
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114 ]]></command> |
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115 <inputs> |
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116 <conditional name="input"> |
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117 <param name="input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> |
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118 <option value="paired">Paired-end FASTQ</option> |
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119 <option value="single">Single-end FASTQ</option> |
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120 <option value="paired_collection">Paired FASTQ Collection</option> |
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121 <option value="aligned">BAM file of aligned reads</option> |
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122 </param> |
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123 <when value="paired"> |
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124 <param name="reads1" type="data" format="@FORMATS@" label="Select first set of reads" help="Specify dataset with forward reads"/> |
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125 <param name="reads2" type="data" format="@FORMATS@" label="Select second set of reads" help="Specify dataset with reverse reads"/> |
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126 <expand macro="params_fastq" /> |
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127 </when> |
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128 <when value="single"> |
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129 <param name="reads" type="data" format="@FORMATS@" label="Select fasta/fastq dataset" help="Specify dataset with single reads"/> |
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130 <expand macro="params_fastq" /> |
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131 </when> |
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132 <when value="paired_collection"> |
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133 <param name="collection" format="@FORMATS@" type="data_collection" collection_type="paired" label="Select a paired collection"/> |
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134 <expand macro="params_fastq" /> |
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135 </when> |
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136 <when value="aligned"> |
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137 <param name="bam" format="sam,bam" type="data" label="Select BAM file(s) with alignments"/> |
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138 <param argument="--coverage" type="integer" min="0" optional="true" value="" label="The desired depth of coverage to subsample the alignment to"/> |
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139 <param type="integer" argument="--step-size" value="100" label="When a region has less than the desired coverage, the step size to move along the chromosome to find more reads." |
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140 help="The lowest of the step and the minimum end coordinate of the reads in the region will be used. This parameter can have a significant impact on the runtime of the subsampling process."/> |
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141 </when> |
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142 </conditional> |
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143 <param type="integer" argument="--seed" optional="true" label="Random seed to use"/> |
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144 </inputs> |
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145 <outputs> |
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146 <data name="paired_output1" label="${tool.name} on ${on_string}: paired-end r1" format_source="reads1"> |
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147 <filter>input['input_selector'] == "paired"</filter> |
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148 </data> |
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149 <data name="paired_output2" label="${tool.name} on ${on_string}: paired-end R2" format_source="reads2"> |
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150 <filter>input['input_selector'] == "paired"</filter> |
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151 </data> |
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152 <data name="single_output" label="${tool.name} on ${on_string}: single-end" format_source="reads"> |
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153 <filter>input['input_selector'] == 'single'</filter> |
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154 </data> |
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155 <collection name="collection_output" type="paired" label="${tool.name} on ${on_string}: paired-collection"> |
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156 <filter>input['input_selector'] == "paired_collection"</filter> |
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157 <data name="forward" label="${tool.name} on ${input.collection.forward.name}: paired-end r1" format_source="collection['forward']"/> |
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158 <data name="reverse" label="${tool.name} on ${input.collection.reverse.name}: paired-end R2" format_source="collection['reverse']"/> |
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159 </collection> |
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160 <data name="bam_output" label="${tool.name} on ${on_string}: BAM" format="bam"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
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161 <filter>input['input_selector'] == 'aligned'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
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162 </data> |
0
49793e8a86f7
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163 </outputs> |
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164 <tests> |
49793e8a86f7
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165 <test expect_num_outputs="1"> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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166 <!-- test 1: single-end fastq by coverage in bases --> |
49793e8a86f7
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167 <conditional name="input"> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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168 <param name="input_selector" value="single"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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169 <param name="reads" value="r1.fastq.gz"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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170 </conditional> |
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171 <conditional name="subsample"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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172 <param name="type" value="coverage"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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173 <param name="genome_size_unit" value="b"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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174 <param name="genome_size" value="1000"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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175 <param name="coverage" value="1"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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176 </conditional> |
49793e8a86f7
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177 <param name="seed" value="1"/> |
49793e8a86f7
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178 <output name="single_output" value="single_by_coverage_b.fastq.gz" ftype="fastqsanger.gz"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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179 </test> |
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180 <test expect_num_outputs="2"> |
49793e8a86f7
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181 <!-- test 2: paired-end fastq by coverage in kb --> |
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182 <conditional name="input"> |
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183 <param name="input_selector" value="paired"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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184 <param name="reads1" value="r1.fastq.gz"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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185 <param name="reads2" value="r2.fastq.gz"/> |
49793e8a86f7
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186 </conditional> |
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187 <conditional name="subsample"> |
49793e8a86f7
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188 <param name="type" value="coverage"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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189 <param name="genome_size_unit" value="k"/> |
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190 <param name="genome_size" value="1"/> |
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191 <param name="coverage" value="1"/> |
49793e8a86f7
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192 </conditional> |
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193 <param name="seed" value="1"/> |
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194 <output name="paired_output1" value="paired1_by_coverage_k.fastq.gz" ftype="fastqsanger.gz"/> |
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195 <output name="paired_output2" value="paired2_by_coverage_k.fastq.gz" ftype="fastqsanger.gz"/> |
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196 </test> |
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197 <test expect_num_outputs="3"> |
3
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198 <!-- test 3: paired-collection fastq by coverage in mb --> |
0
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199 <conditional name="input"> |
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200 <param name="input_selector" value="paired_collection"/> |
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201 <param name="collection"> |
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202 <collection type="paired"> |
49793e8a86f7
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203 <element name="forward" value="r1.fastq.gz"/> |
49793e8a86f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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204 <element name="reverse" value="r2.fastq.gz"/> |
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205 </collection> |
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206 </param> |
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207 </conditional> |
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208 <conditional name="subsample"> |
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209 <param name="type" value="coverage"/> |
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210 <param name="genome_size_unit" value="m"/> |
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211 <param name="genome_size" value="0.001"/> |
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212 <param name="coverage" value="1"/> |
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213 </conditional> |
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214 <param name="seed" value="1"/> |
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215 <output_collection name="collection_output" type="paired"> |
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216 <element name="forward" file="paired1_by_coverage_m.fastq.gz" ftype="fastqsanger.gz"/> |
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217 <element name="reverse" file="paired2_by_coverage_m.fastq.gz" ftype="fastqsanger.gz"/> |
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218 </output_collection> |
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219 </test> |
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220 <test expect_num_outputs="1"> |
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221 <!-- test 4: single-end fasta by coverage in gb --> |
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222 <conditional name="input"> |
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223 <param name="input_selector" value="single"/> |
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224 <param name="reads" value="r1.fasta.gz"/> |
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225 </conditional> |
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226 <conditional name="subsample"> |
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227 <param name="type" value="coverage"/> |
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228 <param name="genome_size_unit" value="g"/> |
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229 <param name="genome_size" value="0.001"/> |
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230 <param name="coverage" value="0.001"/> |
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231 </conditional> |
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232 <param name="seed" value="1"/> |
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233 <output name="single_output" value="single_end_by_coverage_g.fasta" ftype="fasta.gz"/> |
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234 </test> |
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235 <test expect_num_outputs="2"> |
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236 <!-- test 5: paired-end fastq by number of bases --> |
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237 <conditional name="input"> |
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238 <param name="input_selector" value="paired"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 547fd33a419af07f6f90a2daa2c00fa82b1d3ae5
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239 <param name="reads1" value="r1.fastq"/> |
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240 <param name="reads2" value="r2.fastq"/> |
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241 </conditional> |
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242 <conditional name="subsample"> |
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243 <param name="type" value="num_bases"/> |
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244 <param name="num_bases_unit" value="k"/> |
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245 <param name="bases" value="2"/> |
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246 </conditional> |
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247 <param name="seed" value="1"/> |
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248 <output name="paired_output1" value="paired1_by_num_bases_k.fastq" ftype="fastqsanger"/> |
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249 <output name="paired_output2" value="paired2_by_num_bases_k.fastq" ftype="fastqsanger"/> |
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250 </test> |
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251 <test expect_num_outputs="2"> |
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252 <!-- test 6: paired-end fasta by number of reads --> |
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253 <conditional name="input"> |
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254 <param name="input_selector" value="paired"/> |
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255 <param name="reads1" value="r1.fasta.gz"/> |
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256 <param name="reads2" value="r2.fasta.gz"/> |
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257 </conditional> |
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258 <conditional name="subsample"> |
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259 <param name="type" value="num_reads"/> |
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260 <param name="num" value="5"/> |
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261 </conditional> |
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262 <param name="seed" value="1"/> |
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263 <output name="paired_output1" value="paired1_by_num_reads.fasta.gz" ftype="fasta.gz"/> |
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264 <output name="paired_output2" value="paired2_by_num_reads.fasta.gz" ftype="fasta.gz"/> |
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265 </test> |
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266 <test expect_num_outputs="3"> |
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267 <!-- test 7: paired-collection fasta by fraction reads --> |
0
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268 <conditional name="input"> |
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269 <param name="input_selector" value="paired_collection"/> |
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270 <param name="collection"> |
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271 <collection type="paired"> |
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272 <element name="forward" value="r1.fasta"/> |
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273 <element name="reverse" value="r2.fasta"/> |
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274 </collection> |
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275 </param> |
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276 </conditional> |
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277 <conditional name="subsample"> |
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278 <param name="type" value="frac_reads"/> |
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279 <param name="frac" value="0.6"/> |
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280 </conditional> |
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281 <param name="seed" value="1"/> |
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282 <output_collection name="collection_output" type="paired"> |
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283 <element name="forward" file="paired1_by_frac_reads.fasta" ftype="fasta"/> |
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284 <element name="reverse" file="paired2_by_frac_reads.fasta" ftype="fasta"/> |
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285 </output_collection> |
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286 </test> |
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287 <test expect_num_outputs="1"> |
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288 <!-- test 8: bam input --> |
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289 <conditional name="input"> |
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290 <param name="input_selector" value="aligned"/> |
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291 <param name="bam" value="input.bam" /> |
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292 </conditional> |
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293 <param name="coverage" value="1"/> |
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294 <param name="seed" value="1"/> |
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295 <output name="bam_output" value="output.bam" ftype="bam"/> |
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296 </test> |
0
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297 </tests> |
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298 <help><![CDATA[ |
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299 |
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300 Randomly subsample reads to a specified coverage. Rasusa provides a random subsample of a read file (FASTA or FASTQ), with two ways of |
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301 specifying the size of the subset: |
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302 |
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303 * takes a genome size and the desired coverage |
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304 * takes a target number of bases (nucleotides) or fraction of reads to be sampled |
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305 ]]></help> |
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306 <citations> |
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307 <citation type="doi">10.21105/joss.03941</citation> |
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308 </citations> |
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309 </tool> |