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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper" name="FlaiMapper" version="1.1.2.a">
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3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
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4 <requirements>
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5 <requirement type="package" version="0.7.7">pysam</requirement>
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6 <!--
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7 <requirement type="package" version="0.8.1">pysam</requirement>
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8 -->
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9 <requirement type="package" version="1.1.2">flaimapper</requirement>
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10 </requirements>
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11
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12 <version_command>flaimapper --version</version_command>
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13
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14 <command>
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15 flaimapper
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16 -v
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17 -f $output_format
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18 -o $output
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19 -m $mask
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20 -r $fasta
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21
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22 #for $alignment in $alignments
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23 $alignment
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24 #end for
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25 </command>
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26
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27 <inputs>
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28 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
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29
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30 <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
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31
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32 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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33
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34 <param name="output_format" type="select" label="Output format">
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35 <option value="1">Tabular (1 fragment per column)</option>
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36 <option value="2">Tabular (1 precursor per column)</option>
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37 <option value="3">GenBank</option>
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38 <!-- option value="gtf">GTF/GFF</option -->
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39 </param>
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40 </inputs>
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41
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42 <outputs>
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43 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
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44 </outputs>
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45
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46 <help>
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47 You must have 'easy_install' installed.
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48
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49 FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
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50
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51 doi:10.1093/bioinformatics/btu696
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52 </help>
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53 </tool> |
