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1 <tool id='align_and_estimate_abundance' name='Align and Estimate Abundance' version='r20140717'>
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2
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3 <description> using utility align_and_estimate_abundance.pl</description>
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4
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5 <requirements>
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6 <requirement type="package" version="r20140717">trinityrnaseq</requirement>
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7 <requirement type="package" version="0.12.7">bowtie</requirement>
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8 <requirement type="package" version="2.1">samtools</requirement>
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9 <requirement type="package" version="1.5.1">eXpress</requirement>
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10 </requirements>
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11
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12 <command> \$TRINITY_HOME/util/align_and_estimate_abundance.pl
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13 --transcripts $transcripts
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14 --est_method $est_method
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15 --aln_method $aln_method
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16 --prep_reference
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17
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18 ## Inputs.
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19 #if str($reads.paired_or_single) == "paired":
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20
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21 --left $reads.left_input --right $reads.right_input
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22
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23 #if $reads.left_input.ext == 'fa':
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24 --seqType fa
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25 #else:
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26 --seqType fq
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27 #end if
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28
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29 ## Additional parameters.
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30 #if str($reads.optional.use_options) == "yes":
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31
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32 #if str($reads.optional.library_type) != "None":
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33 --SS_lib_type $reads.optional.library_type
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34 #end if
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35
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36
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37
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38 #end if
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39
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40 #else:
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41 --single $reads.input
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42
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43 #if str($reads.input.ext) == 'fa':
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44 --seqType fa
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45 #else:
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46 --seqType fq
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47 #end if
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48
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49 ## Additional parameters.
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50 #if str($reads.optional.use_option) == "yes":
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51
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52 #if str($reads.additional_params.library_type) != "None":
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53 --SS_lib_type $reads.optional.library_type
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54 #end if
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55
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56 #end if
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57 #end if
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58
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59 ## direct to output
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60 > $align_and_estimate_abundance_log 2>&1
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61
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62 </command>
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