Mercurial > repos > iuc > seqtk
annotate seqtk_sample.xml @ 6:288f7f69fe25 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
author | iuc |
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date | Fri, 06 Sep 2019 09:10:07 -0400 |
parents | a09586d5149a |
children | 3da72230c066 |
rev | line source |
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0 | 1 <?xml version="1.0"?> |
6
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
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2 <tool id="seqtk_sample" name="seqtk_sample" version="@TOOL_VERSION@.2"> |
1 | 3 <description>random subsample of fasta or fastq sequences</description> |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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4 <macros> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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5 <import>macros.xml</import> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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6 </macros> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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7 <expand macro="requirements"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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8 <expand macro="stdio"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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9 <command><![CDATA[ |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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10 seqtk sample |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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11 -s $s |
6
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
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12 $advanced.single_pass_mode |
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bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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13 '$in_file' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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14 $subsample_size |
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ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
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15 @CONDITIONAL_GZIP_OUT@ |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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16 ]]></command> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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17 <inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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18 <expand macro="in_faq" /> |
6
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
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19 <param argument="-s" type="integer" value="4" label="RNG seed" help="The seed used for the random number generator. Manually specifying a number here is useful for reproducing the same subsampling in different runs (e.g. read 1 and read 2)" /> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
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20 <param name="subsample_size" type="float" value="100" label="Subsample (decimal fraction or number)" help="Use an integer > 1 to select a specific number of reads. Use a decimal (e.g. 0.5) to select a fraction of reads"/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
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21 <section name="advanced" title="Advanced options" expanded="false"> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
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22 <param name="single_pass_mode" type="boolean" truevalue="" falsevalue="-2" checked="false" label="Enable 1-pass mode" help="Use this if the number of reads you want to sample is small enough to fit into memory. If you're not sure, don't use this."/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
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changeset
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23 </section> |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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changeset
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24 </inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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changeset
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25 <outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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diff
changeset
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26 <data name="default" format_source="in_file" label="Subsample of reads from $in_file.name"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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27 </outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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28 <tests> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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29 <test> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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30 <param name="in_file" value="seqtk_sample.fa"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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31 <param name="subsample_size" value="4"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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32 <param name="s" value="4"/> |
6
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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33 <param name="advanced|single_pass_mode" value="True"/> |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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34 <output name="default" file="seqtk_sample.out" ftype="fasta"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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35 </test> |
4
ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents:
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36 <test> |
ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents:
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diff
changeset
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37 <param name="in_file" value="seqtk_sample.fa.gz" ftype="fasta.gz"/> |
ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents:
3
diff
changeset
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38 <param name="subsample_size" value="4"/> |
ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents:
3
diff
changeset
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39 <param name="s" value="4"/> |
6
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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40 <param name="advanced|single_pass_mode" value='True'/> |
4
ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents:
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41 <output name="default" file="seqtk_sample.out.gz" ftype="fasta.gz"/> |
ecf1c30da3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents:
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diff
changeset
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42 </test> |
6
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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43 <test> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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44 <param name="in_file" value="seqtk_sample.fa.gz" ftype="fasta.gz"/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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45 <param name="subsample_size" value="4"/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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46 <param name="s" value="4"/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
changeset
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47 <param name="advanced|single_pass_mode" value='False'/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
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48 <output name="default" file="seqtk_sample.lowmem.gz" ftype="fasta.gz"/> |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
parents:
5
diff
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49 </test> |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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50 </tests> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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51 <help><![CDATA[ |
0 | 52 **What it does** |
53 | |
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bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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54 Takes a random subsample of FASTA or FASTQ sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__. |
0 | 55 |
56 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset. | |
57 | |
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288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
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58 Two pass sampling mode reads the input file once to build a list of reads to output then again to output the reads. It is twice as slow, but uses much less RAM. It is only in effect when an integer number of reads (not a fraction) is specified as subsample size. |
288f7f69fe25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
iuc
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59 |
0 | 60 @ATTRIBUTION@ |
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bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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61 ]]></help> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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62 <expand macro="citation" /> |
0 | 63 </tool> |