annotate testing6/align_and_estimate_abundance.xml @ 0:fbafdad29706 draft default tip

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1 <tool id='id_align_and_estimate_abundance' name='align_and_estimate_abundance' version='1.0'>
2 
3 <description>align_and_estimate_abundance</description>
4 
5 <requirements>
6         <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
7         <requirement type="package" version="1.1.17">rsem</requirement>
8         <requirement type="package" version="1.5.1">eXpress</requirement>
9         <requirement type="package" version="2.1.0">bowtie2</requirement>
10         <requirement type="package" version="0.12.7">bowtie</requirement>
11         <requirement type="package" version="0.1.18">samtools</requirement>
12         <requirement type="set_environment">TRINITY_HOME</requirement>
13 
14 </requirements>
15 <command >perl \$TRINITY_HOME/util/align_and_estimate_abundance.pl
16 	--transcripts $transcripts
17 	--est_method $est_method
18 	--aln_method $aln_method
19 	--prep_reference
20 
21 	## Inputs.
22 	#if str($reads.paired_or_single) == "paired":
23 
24 	        --left $reads.left_input --right $reads.right_input
25 	
26         	#if  $reads.left_input.ext == 'fa':
27         		--seqType fa
28 	        #else:
29         	        --seqType fq
30 	        #end if
31 
32 		## Additional parameters.
33         	#if str($reads.optional.use_options) == "yes":
34 
35 	                #if str($reads.optional.library_type) != "None":
36         	      		--SS_lib_type $reads.optional.library_type
37                 	#end if
38 			
39 			
40 
41         	#end if
42 
43         #else:
44         	--single $reads.input
45 
46 	        #if  str($reads.input.ext) == 'fa':
47         	     --seqType fa
48 	       	#else:
49        		     --seqType fq
50 	        #end if
51 
52                 ## Additional parameters.
53                 #if str($reads.optional.use_option) == "yes":
54 
55                         #if str($reads.additional_params.library_type) != "None":
56 	                        --SS_lib_type $reads.optional.library_type
57                         #end if
58 
59                 #end if
60 	#end if
61 
62 ## direct to output
63 &gt; $align_and_estimate_abundance_log 2&gt;&amp;1
64 	
65 </command>
66 
67 <inputs>
68 
69 <!-- Required -->
70 <param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts &lt; string &gt; ; transcript fasta file"/>
71 
72 <param name="est_method" type="select" display="radio" label="Choose abundance estimation method" help="">
73 	<option value="RSEM" selected="True">RSEM</option>
74 	<option value="eXpress">eXpress</option>
75 </param>
76 
77 <param name="aln_method" type="select" display="radio" label="Choose alignment method" help="">
78 	<option value="bowtie" selected="True">bowtie</option>
79 	<option value="bowtie2">bowtie2</option>
80 </param>
81 	
82 <conditional name="reads">
83 	<param name="paired_or_single" type="select" label="Paired or Single-end reads?">
84 		<option value="paired">Paired</option>
85 		<option value="single">Single</option>
86 	</param>
87 
88 
89 	<when value="paired">
90 		<param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
91 		<param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
92 
93 		<param name="seqtype" type="select" label="--seqType" help="">
94 			<option value='fq' selected='true'>fastq</option>
95 			<option value='fa'>fasta</option> 	
96 		</param>
97 		
98 		<conditional name='optional'>
99 			<param name='use_options' type='select' label='Use Optional parameters?'>
00 				<option value='no'>NO</option>
01 				<option value='yes'>YES</option>
02 			</param>
03 			<when value='no'/>
04 			<when value='yes'>
05 				<param name="library_type" type="select" label="Strand-specific Library Type">
06 					<option value="None">None</option>
07 					<option value="FR">FR</option>
08 					<option value="RF">RF</option>
09 				</param>
10 
11 			
12 				
13 			</when>
14 		</conditional>
15 	</when>
16 
17 	<when value="single">
18 		<param format="fastq" name="input" type="data" label="Single-end reads" help=""/>
19 		<param name="seqtype" type="select" label="--seqType" help="">
20 			<option value='fq' selected='true'>fastq</option>
21 			<option value='fa'>fasta</option> 	
22 		</param>
23 		
24 		<conditional name='optional'>
25 			<param name='use_options' type='select' label='Use Optional parameters?'>
26 				<option value='no'>NO</option>
27 				<option value='yes'>YES</option>
28 			</param>
29 			<when value='no'/>
30 			<when value='yes'>
31 				<param name="library_type" type="select" label="Strand-specific Library Type">
32 					<option value="None">None</option>
33 					<option value="F">F</option>
34 					<option value="R">R</option>
35 				</param>
36 			</when>
37 		</conditional>
38 	</when>
39 </conditional>
40 
41 </inputs>
42 
43 <outputs>
44 	<data format="txt" name="align_and_estimate_abundance_log" label="${tool.name} on ${on_string}: log" />
45 	<data format="bam" name="bowtie_bam" label="${tool.name} on ${on_string}: bam" from_work_dir="bowtie.bam" />
46 	<data format="tabular"  name="rsem_isoforms"  label="${tool.name} on ${on_string}: isoforms" from_work_dir="RSEM.isoforms.results"/>
47 	<data format="tabular"  name="rsem_genes" label="${tool.name} on ${on_string}: genes" from_work_dir="RSEM.genes.results"/>
48 </outputs>
49 </tool>
50