Mercurial > repos > peterjc > mira4_9_mirabait

annotate tools/mira4_9/mirabait/mira4_9_mirabait.xml @ 0:c9269b5803d8 draft default tip

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
author peterjc
date Wed, 07 Oct 2015 10:31:49 -0400
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c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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1 <tool id="mira4_9_mirabait" name="MIRA v4.9 mirabait" version="0.0.1">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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2 <description>Filter reads using kmer matches</description>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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3 <requirements>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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4 <requirement type="binary">mirabait</requirement>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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5 <requirement type="package" version="4.9.5">MIRA</requirement>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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6 </requirements>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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7 <stdio>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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8 <!-- Assume anything other than zero is an error -->
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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9 <exit_code range="1:" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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10 <exit_code range=":-1" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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11 </stdio>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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12 <version_command interpreter="python">mira_check_version.py ${MIRA4_9}mirabait</version_command>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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13 <command interpreter="python">./mira_check_version.py \${MIRA4_9}mirabait 4.9 &amp;&amp;
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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14 ##First checked it is mirabait v4.9 on the path... now actually run it
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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15 ##-----------------------------------------------------------------------
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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16 \${MIRA4_9}mirabait -k "$kmer_length" -n "$min_occurence" -b "$bait_file"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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17 ##-----------------------------------------------------------------------
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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18 ##Must now map Galaxy datatypes to MIRA file types...
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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19 ##exploiting the polymorphic naming of the input read parameter!
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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20 #if $reads.filename.ext.startswith("fastq")
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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21 ##MIRA doesn't like fastqsanger etc, just plain old fastq
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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22 -f fastq -t fastq
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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23 #elif $reads.filename.ext == "mira"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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24 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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25 -f maf -t maf
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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26 #else
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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27 ##MIRA is happy with fasta as name,
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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28 -f "$reads.filename.ext" -t "$reads.filename.ext"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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29 #end if
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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30 ##-----------------------------------------------------------------------
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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31 #if str($output_choice_cond.output_choice)=="both"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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32 -o "$output_pos" -O "$output_neg"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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33 #elif str($output_choice_cond.output_choice)=="pos"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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34 -o "$output_pos"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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35 #elif str($output_choice_cond.output_choice)=="neg"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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36 -i -O "$output_neg"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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37 #end if
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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38 ##-----------------------------------------------------------------------
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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39 ##Do we need to ignore the reverse strand?
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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40 #if str($strand_choice) == "fwd"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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41 -r
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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42 #end if
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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43 ##-----------------------------------------------------------------------
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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44 ##Default is to mark k-mers with upper case...
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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45 #if str($output_case) == "original"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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46 -c
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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47 #end if
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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48 ##-----------------------------------------------------------------------
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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49 #if str($reads.type) == "paired"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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50 #if $reads.filename.ext != $reads.filename2.ext
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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51 ##TODO: Is there a better way to signal an error to Galaxy here?
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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52 ; echo "ERROR: Paired read datatype mis-match!" ; false
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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53 #end if
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54 -p "$reads.filename" "$reads.filename2"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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55 #elif str($reads.type) == "interleaved"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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56 -P "$reads.filename"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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57 #elif str($reads.type) == "none"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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58 "$reads.filename"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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59 #end if
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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60 </command>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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61 <inputs>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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62 <!-- TODO: mirabait now allows multiple input files, and can do multiple outputs - or merge into one? -->
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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63 <!-- TODO: define a new Galaxy datatype for the bait hash file? -->
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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64 <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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65 <conditional name="reads">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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66 <param name="type" type="select" label="Are these paired reads?">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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67 <option value="paired">Paired reads (as two files)</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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68 <option value="interleaved">Paired reads (as one interleaved file)</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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69 <option value="none">Unpaired reads (single or orphan reads as one file)</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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70 </param>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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71 <when value="paired">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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72 <param name="filename" type="data" format="fastq,fasta" required="true" label="Read file one"/>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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73 <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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74 </when>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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75 <when value="interleaved">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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76 <param name="filename" type="data" format="fasta,fastq" required="true" label="Interleaved paired reads to search" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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77 </when>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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78 <when value="none">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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79 <param name="filename" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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80 </when>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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81 </conditional>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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82 <conditional name="output_choice_cond">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
83 <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
84 <option value="both">Both positive matches and negative matches, as two files</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
85 <option value="pos" selected="true">Just positive matches, as a single file</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
86 <option value="neg">Just negative matches, as a single file</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
87 </param>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
88 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
89 <when value="both" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
90 <when value="pos" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
91 <when value="neg" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
92 </conditional>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
93 <param name="output_case" type="select" label="How to use sequence case in output?">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
94 <option value="original">Preserve case from input</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
95 <option value="bait">Mark k-mer matches in upper case</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
96 </param>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
97 <param name="strand_choice" type="select" label="Check for matches on both strands?">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
98 <option value="both">Check both strands</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
99 <option value="fwd">Just forward strand</option>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
100 </param>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
101 <param name="kmer_length" type="integer" value="31" min="1" max="256"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
102 label="k-mer length" help="Maximum 256" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
103 <param name="min_occurence" type="integer" value="1" min="1"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
104 label="Minimum k-mer occurence"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
105 help="How many k-mer matches do you want per read? Minimum one" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
106 </inputs>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
107 <outputs>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
108 <data name="output_pos" format_source="filename" metadata_source="filename"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
109 label="$reads.filename.name #if str($reads.type)=='paired' then 'and $reads.filename2.name' else ''# matching $bait_file.name">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
110 <filter>output_choice_cond["output_choice"] != "neg"</filter>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
111 </data>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
112 <data name="output_neg" format_source="filename" metadata_source="filename"
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
113 label="$reads.filename.name #if str($reads.type)=='paired' then 'and $reads.filename2.name' else ''# not matching $bait_file.name">
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
114 <filter>output_choice_cond["output_choice"] != "pos"</filter>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
115 </data>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
116 </outputs>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
117 <tests>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
118 <test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
119 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
120 <param name="reads|type" value="none" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
121 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
122 <param name="output_choice" value="pos" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
123 <param name="output_case" value="original" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
124 <output name="output_pos" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
125 </test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
126 <test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
127 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
128 <param name="reads|type" value="none" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
129 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
130 <param name="output_case" value="bait" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
131 <output name="output_pos" file="tvc_mini_bait_pos_case.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
132 </test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
133 <test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
134 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
135 <param name="reads|type" value="none" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
136 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
137 <param name="output_case" value="bait" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
138 <output name="output_pos" file="tvc_mini_bait_pos_case.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
139 </test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
140 <test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
141 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
142 <param name="reads|type" value="none" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
143 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
144 <param name="output_case" value="bait" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
145 <param name="kmer_length" value="32" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
146 <param name="min_occurence" value="50" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
147 <output name="output_pos" file="tvc_mini_bait_strict_case.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
148 </test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
149 <test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
150 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
151 <param name="reads|type" value="none" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
152 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
153 <param name="output_choice" value="neg" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
154 <param name="output_case" value="original" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
155 <output name="output_neg" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
156 </test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
157 <test>
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
158 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
159 <param name="reads|type" value="none" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
160 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
161 <param name="output_choice" value="neg" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
162 <param name="output_case" value="bait" />
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
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163 <output name="output_neg" file="tvc_mini_bait_neg_case.fastq" ftype="fastqsanger" />
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164 </test>
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165 <test>
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166 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
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167 <param name="reads|type" value="none" />
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168 <param name="reads|filename" value="tvc_mini.fastq" ftype="fastqsanger" />
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169 <param name="output_choice" value="both" />
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170 <param name="output_case" value="original" />
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171 <output name="output_pos" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
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172 <output name="output_neg" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
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173 </test>
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174 </tests>
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175 <help>
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176 **What it does**
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177
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178 Runs the ``mirabait`` utility from MIRA v4.9 to filter your input reads
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179 according to whether or not they contain perfect kmer matches to your
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180 bait file. By default this looks for 31-mers (kmers or *k*-mers where
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181 the fragment length *k* is 31), and only requires a single matching kmer.
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182
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183 The ``mirabait`` utility is useful in many applications and pipelines
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184 outside of using the main MIRA tool for assembly or mapping.
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185
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186 .. class:: warningmark
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187
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188 Note ``mirabait`` cannot be used on protein (amino acid) sequences.
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189
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190 **Example Usage**
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191
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192 To remove over abundant entries like rRNA sequences, run ``mirabait`` with
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193 known rRNA sequences as the bait and select the *negative* matches.
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194
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195 To do targeted assembly by fishing out reads belonging to a gene and just
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196 assemble these, run ``mirabait`` with the gene of interest as the bait and
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197 select the *positive* matches.
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198
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199 To iteratively reconstruct mitochondria you could start by fishing out reads
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200 matching any known mitochondrial sequence, assembly those, and repeat.
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201
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202
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203 **Notes on paired read**
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204
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205 .. class:: warningmark
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206
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207 Unlike ``mirabait`` from MIRA v4.0, this version is aware of paired reads
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208 and will preserve the pairing (if either the forward or the reverse read
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209 has enough *k*-mer matches, the pair is accepted).
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210
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211
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212 **Citation**
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213
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214 If you use this Galaxy tool in work leading to a scientific publication please
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215 cite the following papers:
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216
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217 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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218 Galaxy tools and workflows for sequence analysis with applications
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219 in molecular plant pathology. PeerJ 1:e167
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220 http://dx.doi.org/10.7717/peerj.167
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221
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222 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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223 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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224 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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225 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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226
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227 This wrapper is available to install into other Galaxy Instances via the Galaxy
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228 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler_4_9
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229 </help>
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230 <citations>
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231 <citation type="doi">10.7717/peerj.167</citation>
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232 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
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233 author = {B. Chevreux and T. Wetter and S. Suhai},
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234 year = {1999},
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235 title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
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236 journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
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237 volume = {99},
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238 pages = {45-56},
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239 url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
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240 }</citation>
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241 </citations>
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242 </tool>