Mercurial > repos > iuc > megan_sam2rma

annotate sam2rma.xml @ 0:4f0a8e401e2e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
author iuc
date Sat, 11 Dec 2021 11:52:57 +0000
parents
children ef0443c0eaba
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4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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1 <tool id="megan_sam2rma" name="MEGAN: Generate a MEGAN rma6 file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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2 <description>from a DIAMOND or MALT sam file</description>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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3 <macros>
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4 <import>macros.xml</import>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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5 </macros>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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6 <expand macro="bio_tools"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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7 <expand macro="requirements"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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8 <command detect_errors="exit_code"><![CDATA[
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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9 #import re
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10
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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11 #if str($input_type_cond.input_type) in ['single', 'pair']:
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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12 #set read1 = $input_type_cond.read1
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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13 #set sam1 = $input_type_cond.sam1
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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14 #else:
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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15 ## Processing paired reads are tricky if we're
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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16 ## downstream from MALT. MALT doesn’t have a
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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17 ## paired-read mode, so it won’t attempt to analyze
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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18 ## reads in pairs. To do paired read processing,
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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19 ## set MALT to generate SAM files and then import the
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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20 ## SAM files into MEGAN, specifying paired read mode
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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21 ## there. If you have multiple SAM files for the same
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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22 ## sample, then import them all at the same time to
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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23 ## create one unified rma6 file.
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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24
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25 #set read1 = $input_type_cond.reads_collection['forward']
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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26 #set sam1 = $input_type_cond.sam1
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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27 #end if
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28
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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29 #if $read1.is_of_type('fasta', 'fasta.gz'):
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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30 #set read_ext = '.fasta'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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31 #else:
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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32 #set read_ext = '.fastq'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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33 #end if
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34 #if $read1.ext.endswith('.gz'):
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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35 #set read_ext = $read_ext + '.gz'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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36 #end if
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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37
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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38 #set read1_identifier = 'read1' + $read_ext
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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39 ln -s '${read1}' '${read1_identifier}' &&
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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40
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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41 #set sam1_identifier = 'sam1.' + $sam1.ext
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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42 ln -s '${sam1}' '${sam1_identifier}' &&
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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43
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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44 #if str($input_type_cond.input_type) in ['pair', 'paired']:
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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45 #if str($input_type_cond.input_type) == 'pair':
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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46 #set read2 = $input_type_cond.read2
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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47 #set sam2 = $input_type_cond.sam2
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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48 #else if str($input_type_cond.input_type) == 'paired':
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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49 #set read2 = $input_type_cond.reads_collection['reverse']
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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50 #set sam2 = $input_type_cond.sam2
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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51 #end if
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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52 #set read2_identifier = 'read2' + $read_ext
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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53 ln -s '${read2}' '${read2_identifier}' &&
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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54 #set sam2_identifier = 'sam2.' + $sam2.ext
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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55 ln -s '${sam2}' '${sam2_identifier}' &&
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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56 #end if
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57
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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58 ## The output must be a directory when we have multiple
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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59 ## inputs, and the outputs inherit the base name of the
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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60 ## inputs.
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61
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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62 sam2rma
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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63 #if str($input_type_cond.input_type) == 'single':
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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64 --in '${sam1_identifier}'
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65 --reads '${read1_identifier}'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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66 --out '${output_single}'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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67 #else if str($input_type_cond.input_type) == 'pair':
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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68 --in '${sam1_identifier}' '${sam2_identifier}'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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69 --reads '${read1_identifier}' '${read2_identifier}'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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70 --paired
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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71 --pairedSuffixLength $input_type_cond.pairedSuffixLength
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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72 --out '.'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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73 #else if str($input_type_cond.input_type) == 'paired':
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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74 --in '${sam1_identifier}' '${sam2_identifier}'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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75 --reads '${read1_identifier}' '${read2_identifier}'
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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76 --paired
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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77 --pairedSuffixLength $input_type_cond.pairedSuffixLength
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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78 ## Strangely, megan requires an output
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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79 ## directory when processing paired reads
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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80 ## even though it produces a single file.
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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81 ## We'll accommodate thie by prepending ./
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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82 ## to a temporary output file and then move
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83 ## it later.
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84 --out '.'
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85 #end if
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86 #if $advanced_options.metaDataFile:
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87 --metaDataFile '$advanced_options.metaDataFile'
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88 #end if
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89 #if str($advanced_options.paired_reads_cond.paired_reads) == 'yes':
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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90 --paired
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91 $advanced_options.paired_reads_cond.pairedSuffixLength
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92 #end if
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93 $advanced_options.longReads
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94 --maxMatchesPerRead $advanced_options.maxMatchesPerRead
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95 $advanced_options.classify
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96 --minScore $advanced_options.minScore
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97 --maxExpected $advanced_options.maxExpected
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98 --topPercent $advanced_options.topPercent
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99 --minSupportPercent $advanced_options.minSupportPercent
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100 --minSupport $advanced_options.minSupport
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101 --minPercentReadCover $advanced_options.minPercentReadCover
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102 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
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103 --minReadLength $advanced_options.minReadLength
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104 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
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105 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
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106 --readAssignmentMode '$advanced_options.readAssignmentMode'
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107 #if $advanced_options.conFile:
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108 --conFile '$advanced_options.conFile'
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109 #end if
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110 #if $advanced_options.mapDB:
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111 --mapDB '$advanced_options.mapDB'
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112 #end if
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113 #if str($advanced_options.only) != '':
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114 --only '$advanced_options.only'
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115 #end if
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116 --useCompression 'false'
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117 --threads \${GALAXY_SLOTS:-8}
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118 --tempStoreDir '.'
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119 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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120 && mv 'sam1.rma6' '$output_forward'
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121 && mv 'sam2.rma6' '$output_reverse'
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122 #end if
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123 ]]></command>
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124 <inputs>
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125 <conditional name="input_type_cond">
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126 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
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127 <option value="single" selected="true">Single dataset</option>
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128 <option value="pair">Dataset pair</option>
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129 <option value="paired">List of dataset pairs</option>
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130 </param>
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131 <when value="single">
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132 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by DIAMOND or MALT to generate the SAM file below"/>
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133 <param name="sam1" type="data" format="sam" label="Output file of DIAMOND or MALT on input forward read file"/>
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134 </when>
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135 <when value="pair">
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136 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by DIAMOND or MALT to generate the SAM file below"/>
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137 <param name="sam1" type="data" format="sam" label="Output file of DIAMOND or MALT on input forward read file"/>
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138 <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by DIAMOND or MALT to generate the SAM file below"/>
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139 <param name="sam2" type="data" format="sam" label="Output file of DIAMOND or MALT on input reverse read file"/>
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140 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
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141 </when>
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142 <when value="paired">
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143 <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
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144 <param name="sam1" type="data" format="sam" label="Output file of DIAMOND or MALT on input forward read file"/>
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145 <param name="sam2" type="data" format="sam" label="Output file of DIAMOND or MALT on input reverse read file"/>
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146 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
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147 </when>
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148 </conditional>
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149 <section name="advanced_options" title="Advanced options" expanded="false">
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150 <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
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151 <conditional name="paired_reads_cond">
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152 <param name="paired_reads" type="select" label="DAA file was created using paired reads?">
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153 <option value="no" selected="true">no</option>
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154 <option value="yes">Yes</option>
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155 </param>
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156 <when value="no"/>
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157 <when value="yes">
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158 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
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159 </when>
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160 </conditional>
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161 <expand macro="long_reads_param"/>
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162 <expand macro="max_matches_per_read_param"/>
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163 <expand macro="classify_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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164 <expand macro="min_score_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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165 <expand macro="max_expected_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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166 <expand macro="top_percent_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
167 <expand macro="min_max_params"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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168 <expand macro="lca_params"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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169 <expand macro="read_assignment_mode_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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170 <expand macro="con_file_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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171 <expand macro="mapdb_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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172 <expand macro="only_named_classifications_param"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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173 </section>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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174 </inputs>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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175 <outputs>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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176 <data name="output_single" format="rma6">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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177 <filter>input_type_cond['input_type'] == 'single'</filter>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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178 </data>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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179 <data name="output_forward" format="rma6" label="${tool.name} on ${on_string} (forward">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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180 <filter>input_type_cond['input_type'] != 'single'</filter>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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181 </data>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
182 <data name="output_reverse" format="rma6" label="${tool.name} on ${on_string} (reverse)">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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183 <filter>input_type_cond['input_type'] != 'single'</filter>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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184 </data>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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185 </outputs>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
186 <tests>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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187 <!-- Single dataset input -->
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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188 <test expect_num_outputs="1">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
189 <param name="sam1" ftype="sam" value="input1.sam"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
190 <param name="read1" ftype="fastqsanger.gz" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
191 <output name="output_single" ftype="rma6">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
192 <assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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193 <has_size value="885"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
194 </assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
195 </output>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
196 </test>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
197 <!-- Dataset pair input -->
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
198 <test expect_num_outputs="2">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
199 <param name="input_type" value="pair"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
200 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
201 <param name="sam1" value="input1.sam" ftype="sam"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
202 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
203 <param name="sam2" value="input2.sam" ftype="sam"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
204 <output name="output_forward" ftype="rma6">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
205 <assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
206 <has_size value="805"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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207 </assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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208 </output>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
209 <output name="output_reverse" ftype="rma6">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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210 <assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
211 <has_size value="805"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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212 </assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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213 </output>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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214 </test>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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215 <!-- List of dataset pairs input -->
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
216 <test expect_num_outputs="2">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
217 <param name="input_type" value="paired"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
218 <param name="reads_collection">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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219 <collection type="paired">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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220 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
221 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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222 </collection>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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223 </param>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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224 <param name="sam1" value="input1.sam" ftype="sam"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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225 <param name="sam2" value="input2.sam" ftype="sam"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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226 <output name="output_forward" ftype="rma6">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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227 <assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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228 <has_size value="805"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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229 </assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
230 </output>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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parents:
diff changeset
231 <output name="output_reverse" ftype="rma6">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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232 <assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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233 <has_size value="805"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
234 </assert_contents>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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235 </output>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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236 </test>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
237 </tests>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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238 <help>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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239 **What it does**
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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240
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
241 Generates a MEGAN RMA (RealMedia Audio) file from a SAM file that was generated by DIAMOND or MALT. MEGAN uses an
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
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diff changeset
242 update of the original RMA file format known as RMA6.
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
243
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
244 Inputs consist of reads in fasta or fasqsanger format (gzip compression is supported) and associated SAM files.
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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245 Each read file should have been used previously as the input to DIAMOND or MALT to produce the associated SAM file
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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diff changeset
246 for this tool.
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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247 </help>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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248 <expand macro="citations"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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249 </tool>