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annotate tools/mentalist_call/mentalist_call.xml @ 30:d6619ce444f9 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7439570c55ac2a400c96d05135ab86d499fd612a-dirty
author dfornika
date Mon, 04 Dec 2017 18:36:05 -0500
parents 25baf4a4b98e
children 038558f760a0
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d6619ce444f9 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7439570c55ac2a400c96d05135ab86d499fd612a-dirty
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1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3">
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2 <requirements>
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3 <requirement type="package" version="0.1.3">mentalist</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 mentalist
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7 call
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8 -o '$output_file'
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9 --db '$kmer_db.fields.path'
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10 #if $discard_threshold
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11 -t '$discard_threshold'
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12 #end if
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13 #if $input_type.sPaired == "paired":
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14 -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
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15 #elif $input_type.sPaired == "collections":
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16 -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <conditional name="input_type">
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21 <param name="sPaired" type="select" label="Single Pair or Collection">
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22 <option value="collections">Paired-end Collections</option>
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23 <option value="paired">Paired-end</option>
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24 </param>
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25 <when value="paired">
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26 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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27 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
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28 </when>
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29 <when value="collections">
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30 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
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31 </when>
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32 </conditional>
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33 <param name="kmer_db" type="select">
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34 <options from_data_table="mentalist_databases">
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35 <validator type="no_options" message="No MentaLiST databases are available" />
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36 </options>
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37 </param>
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38 <param name="discard_threshold" type="float"
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39 label="Discard Threshold" help="A read of length L is discarded if it has at less than (L - k) * t hits to the same locus in the kmer database, where k is the kmer length. 0 &lt;= t &lt;= 1"
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40 value="0.3" min="0" max="1" />
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41 <param name="skip_length" type="integer"
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42 label="Skip Length" help="Skip length between consecutive k-mers."
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43 value="1" min="1" max="32" />
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44 </inputs>
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45 <outputs>
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46 <data name="output_file" format="tabular"/>
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47 </outputs>
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48 <help><![CDATA[
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49 ]]></help>
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50 <citations>
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51 <citation type="doi">10.1101/172858</citation>
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52 </citations>
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53 </tool>