Mercurial > repos > iuc > fastk_fastk

annotate fastk.xml @ 0:ff827f983bbb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
author iuc
date Fri, 03 May 2024 20:23:04 +0000
parents
children b820ef95ca20
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0
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
iuc
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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
iuc
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3 <macros>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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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
iuc
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5 </macros>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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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
iuc
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7 <command detect_errors="exit_code"><![CDATA[
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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8 mkdir -p outfiles/tmpfiles &&
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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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
iuc
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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
iuc
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11 #elif $infile.is_of_type("fastq.gz"):
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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12 #set INPUTFILE="input.fastq.gz"
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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13 #else
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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14 #set INPUTFILE="input."+$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
iuc
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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
iuc
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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
iuc
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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
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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24 -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/tmpfiles
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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25 #if $sorted_table.sorted_table_option == 'yes_with_default':
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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26 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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27 #elif $sorted_table.sorted_table_option == 'yes_with_custom':
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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28 && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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29 #end if
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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30 && 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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31 ]]></command>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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32 <inputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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33 <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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34 <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40" />
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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35 <conditional name="sorted_table">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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36 <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
iuc
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37 <option value="no">No</option>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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38 <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
iuc
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39 <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
iuc
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40 </param>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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41 <when value="no"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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42 <when value="yes_with_default">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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43 <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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44 </when>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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45 <when value="yes_with_custom">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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46 <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
iuc
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47 <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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48 </when>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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49 </conditional>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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50 </inputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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51 <outputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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52 <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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53 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist" />
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
iuc
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54 <data name="tabex_hist" format="txt" label="${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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55 <filter> sorted_table['sorted_table_option'] != 'no' </filter>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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56 </data>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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57 </outputs>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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58 <tests>
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59 <!-- TEST 1 -->
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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60 <test expect_num_outputs="2">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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61 <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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62 <output name="fastk_out" ftype="tar">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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63 <assert_contents>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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64 <has_archive_member path="./outfiles/output.hist"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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65 </assert_contents>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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66 </output>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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67 </test>
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68 <!-- TEST 2 -->
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69 <test expect_num_outputs="3">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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70 <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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71 <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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72 <param name="sorted_table_option" 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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73 </conditional>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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74 <output name="fastk_out" ftype="tar">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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75 <assert_contents>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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76 <has_archive_member path="./outfiles/output.hist"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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77 <has_archive_member path="./outfiles/output.ktab"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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78 </assert_contents>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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79 </output>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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80 <output name="tabex_hist" value="test02.tabex.txt"/>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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81 </test>
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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82 <!-- TEST 3 -->
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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83 <test expect_num_outputs="3">
ff827f983bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
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84 <param name="infile" value="input01.fasta.gz"/>
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85 <conditional name="sorted_table">
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86 <param name="sorted_table_option" value="yes_with_custom"/>
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87 <param name="sorted_table_cutoff" value="5"/>
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88 </conditional>
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89 <output name="fastk_out" ftype="tar">
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90 <assert_contents>
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91 <has_archive_member path="./outfiles/output.hist"/>
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92 <has_archive_member path="./outfiles/output.ktab"/>
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93 </assert_contents>
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94 </output>
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95 <output name="tabex_hist" value="test03.tabex.txt"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99 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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100
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101 The input data can be in CRAM, BAM, SAM, fasta, or fastq files.
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102
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103 FastK produces the following outputs:
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104
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105 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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106
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107 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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108
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109 3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
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110
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111
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112 ]]></help>
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113 <expand macro="citations"/>
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114 </tool>