Mercurial > repos > nikos > hrf_seq

annotate estimate_unique_counts.xml @ 2:14d6929f8aa1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Tool tests or/and test-data are missing.
author nikos
date Thu, 11 Sep 2014 08:30:05 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
1 <tool id="hrf_euc" version="0.1" name="Estimate Unique Counts" force_history_refresh="True">
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
2 <description></description>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
3 <requirements>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
4 <requirement type="package" version="0.1.18">samtools</requirement>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
5 </requirements>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
6 <command interpreter="bash">
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
7 estimate_unique_counts.sh
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
8
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
9 ## Inputs
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
10 -f $input1 -b $input2
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
11
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
12 ##
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
13 #if str( $priming.flag ) == 'False':
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
14 -p -1
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
15 #else
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
16 -p $priming.position
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
17 #end if
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
18
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
19 </command>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
20
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
21 <inputs>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
22 <param format="bam" name="input1" type="data" label="Aligned Reads" help="BAM format." />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
23 <param format="tabular" name="input2" type="data" label="Barcodes" help="Produced by Debarcoding tool." />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
24 <conditional name="priming">
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
25 <param name="flag" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Set priming position" help="Set all reads to have a specific priming position." />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
26 <when value="True">
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
27 <param name="position" type="integer" value="-1" label="Priming position" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
28 </when>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
29 </conditional>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
30 </inputs>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
31
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
32 <outputs>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
33 <data format="tabular" name="trimming_stats" label="${tool.name} on ${on_string}: Trimming stats" from_work_dir="output_dir/trimming_stats.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
34 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" from_work_dir="output_dir/summary.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
35 <data format="tabular" name="unique_barcodes" label="${tool.name} on ${on_string}: Unique Barcodes" from_work_dir="output_dir/unique_barcodes.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
36 <data format="tabular" name="read_counts" label="${tool.name} on ${on_string}: Read Counts" from_work_dir="output_dir/read_counts.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
37 </outputs>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
38
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
39 <tests>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
40 <test>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
41 <param name="input1" value="sample.bam" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
42 <param name="input2" value="barcodes.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
43 <output name="trimming_stats" file="trimming_stats.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
44 <output name="summary" file="summary.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
45 <output name="unique_barcodes" file="unique_barcodes.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
46 <output name="read_counts" file="read_counts.txt" />
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
47 </test>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
48 </tests>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
49
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
50 <help>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
51 </help>
14d6929f8aa1 Tool tests or/and test-data are missing.
nikos
parents:
diff changeset
52 </tool>