Mercurial > repos > anmoljh > align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 1:16aaa05e7d67 draft

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author anmoljh
date Thu, 27 Aug 2015 12:35:23 -0400
parents 972c930ed278
children 96a9a03f8948
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0:972c930ed278 1:16aaa05e7d67
59 ## direct to output 59 ## direct to output
60 > $align_and_estimate_abundance_log 2>&1 60 > $align_and_estimate_abundance_log 2>&1
61 61
62 </command> 62 </command>
63 63
64 <inputs>
65
66 <!-- Required -->
67 <param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts &lt; string &gt; ; transcript fasta file"/>
68
69 <param name="est_method" type="select" display="radio" label="Choose abundance estimation method" help="">
70 <option value="RSEM" selected="True">RSEM</option>
71 <option value="eXpress">eXpress</option>
72 </param>
73
74 <param name="aln_method" type="select" display="radio" label="Choose alignment method" help="">
75 <option value="bowtie" selected="True">bowtie</option>
76 <option value="bowtie2">bowtie2</option>
77 </param>
78
79 <conditional name="reads">
80 <param name="paired_or_single" type="select" label="Paired or Single-end reads?">
81 <option value="paired">Paired</option>
82 <option value="single">Single</option>
83 </param>
84
85
86 <when value="paired">
87 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
88 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
89
90 <param name="seqtype" type="select" label="--seqType" help="">
91 <option value='fq' selected='true'>fastq</option>
92 <option value='fa'>fasta</option>
93 </param>
94
95 <conditional name='optional'>
96 <param name='use_options' type='select' label='Use Optional parameters?'>
97 <option value='no'>NO</option>
98 <option value='yes'>YES</option>
99 </param>
100 <when value='no'/>
101 <when value='yes'>
102 <param name="library_type" type="select" label="Strand-specific Library Type">
103 <option value="None">None</option>
104 <option value="FR">FR</option>
105 <option value="RF">RF</option>
106 </param>
107
108
109
110 </when>
111 </conditional>
112 </when>
113 <when value="single">
114 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
115 <param name="seqtype" type="select" label="--seqType" help="">
116 <option value='fq' selected='true'>fastq</option>
117 <option value='fa'>fasta</option>
118 </param>
119
120 <conditional name='optional'>
121 <param name='use_options' type='select' label='Use Optional parameters?'>
122 <option value='no'>NO</option>
123 <option value='yes'>YES</option>
124 </param>
125 <when value='no'/>
126 <when value='yes'>
127 <param name="library_type" type="select" label="Strand-specific Library Type">
128 <option value="None">None</option>
129 <option value="F">F</option>
130 <option value="R">R</option>
131 </param>
132 </when>
133 </conditional>
134 </when>
135 </conditional>
136
137 </inputs>
138
139 <outputs>
140 <data format="txt" name="align_and_estimate_abundance_log" label="${tool.name} on ${on_string}: log" />
141 <data format="bam" name="bowtie_bam" label="${tool.name} on ${on_string}: bam" from_work_dir="bowtie.bam" />
142 <data format="tabular" name="rsem_isoforms" label="${tool.name} on ${on_string}: isoforms" from_work_dir="RSEM.isoforms.results"/>
143 <data format="tabular" name="rsem_genes" label="${tool.name} on ${on_string}: genes" from_work_dir="RSEM.genes.results"/>
144 </outputs>
145 </tool>
146