Mercurial > repos > iuc > fastk_fastk

annotate fastk.xml @ 1:b820ef95ca20 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
author iuc
date Tue, 14 May 2024 12:47:29 +0000
parents ff827f983bbb
children 87f4b4dced3e
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ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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1 <tool id="fastk_fastk" name="FastK" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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2 <description>A k-mer counter for high-quality assembly datasets</description>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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3 <macros>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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4 <import>macros.xml</import>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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5 </macros>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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6 <expand macro="requirements" />
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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7 <command detect_errors="exit_code"><![CDATA[
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b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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8 mkdir -p outfiles/ktabfiles &&
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ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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9 #if $infile.is_of_type("fastq"):
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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10 #set INPUTFILE="input.fastq"
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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11 #elif $infile.is_of_type("fastq.gz"):
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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12 #set INPUTFILE="input.fastq.gz"
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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13 #else
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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14 #set INPUTFILE="input."+$infile.ext
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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15 #end if
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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16 ln -s '$infile' $INPUTFILE &&
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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17 FastK $INPUTFILE
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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18 -k$kmer_size
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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19 #if $sorted_table.sorted_table_option == 'yes_with_default':
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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20 -t
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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21 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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22 -t$sorted_table_cutoff
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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23 #end if
1
b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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24 -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/ktabfiles
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ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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25 #if $sorted_table.sorted_table_option == 'yes_with_default':
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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26 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
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b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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27 && mv outfiles/.*.ktab* outfiles/ktabfiles
b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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28 && mv outfiles/*.ktab outfiles/ktabfiles
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ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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29 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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30 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
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b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
iuc
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31 && mv outfiles/.*.ktab* outfiles/ktabfiles
b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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32 && mv outfiles/*.ktab outfiles/ktabfiles
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ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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33 #end if
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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34 && tar -c -f fastk.tar ./outfiles/
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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35 ]]></command>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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36 <inputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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37 <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>
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b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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38 <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40"/>
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ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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39 <conditional name="sorted_table">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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40 <param name="sorted_table_option" type="select" label="Sort table" help="Do you want a sorted table of all canonical k-mers and their counts? The sorted table is sorted lexicographically on the k-mer where a &lt; c &lt; g &lt; t.">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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41 <option value="no">No</option>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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42 <option value="yes_with_default">Yes, Default sorted </option>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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43 <option value="yes_with_custom">Yes, Custom sorted </option>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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44 </param>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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45 <when value="no"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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46 <when value="yes_with_default">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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47 <param name="tabex_threshold_for_default" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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48 </when>
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49 <when value="yes_with_custom">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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50 <param name="sorted_table_cutoff" type="integer" min="2" value="10" label="Enter sorted table cutoff value"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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51 <param name="tabex_threshold_for_custom" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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52 </when>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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53 </conditional>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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54 </inputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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55 <outputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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56 <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/>
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57 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist"/>
b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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58 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="outfiles/ktabfiles/output.ktab" label="${tool.name} on ${on_string}: FastK ktab">
b820ef95ca20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit dbdc7c7b584e6fc578845aaf30bc0498353716f7
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59 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
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60 </data>
0
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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61 <data name="tabex_hist" format="txt" label="${tool.name} on ${on_string}: Tabex output">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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62 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <!-- TEST 1 -->
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67 <test expect_num_outputs="2">
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68 <param name="infile" value="input01.fasta.gz"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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69 <output name="fastk_out" ftype="tar">
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70 <assert_contents>
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71 <has_archive_member path="./outfiles/output.hist"/>
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72 </assert_contents>
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73 </output>
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74 </test>
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75 <!-- TEST 2 -->
1
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76 <test expect_num_outputs="4">
0
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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77 <param name="infile" value="input01.fasta.gz"/>
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78 <conditional name="sorted_table">
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79 <param name="sorted_table_option" value="yes_with_default"/>
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80 </conditional>
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81 <output name="fastk_out" ftype="tar">
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82 <assert_contents>
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83 <has_archive_member path="./outfiles/output.hist"/>
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84 <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
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85 </assert_contents>
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86 </output>
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87 <output name="tabex_hist" file="test02.tabex.txt"/>
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88 </test>
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89 <!-- TEST 3 -->
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90 <test expect_num_outputs="4">
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91 <param name="infile" value="input01.fasta.gz"/>
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92 <conditional name="sorted_table">
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93 <param name="sorted_table_option" value="yes_with_custom"/>
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94 <param name="sorted_table_cutoff" value="5"/>
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95 </conditional>
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96 <output name="fastk_out" ftype="tar">
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97 <assert_contents>
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98 <has_archive_member path="./outfiles/output.hist"/>
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99 <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
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100 </assert_contents>
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101 </output>
1
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102 <output name="tabex_hist" file="test03.tabex.txt"/>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106 FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
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107
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108 The input data can be in CRAM, BAM, SAM, fasta, or fastq files.
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109
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110 FastK produces the following outputs:
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111
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112 1. FastK hist: file in binary format containing histogram information detailing the frequency of occurrence for each k‑mer within the dataset.
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113
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114 2. A Tabex txt file comprising a table of k‑mer/count pairs, sorted lexicographically on the k‑mer sequence, followingthe order a < c < g < t
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115
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116 3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
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117
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118
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119 ]]></help>
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120 <expand macro="citations"/>
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121 </tool>