concatenate: concatenate.xml annotate

annotate concatenate.xml @ 8:323f676857c8 draft default tip

Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.

author	trinity_ctat
date	Fri, 06 Oct 2017 10:55:19 -0400
parents	43cb585e9e1c
children

rev	line source
8 323f676857c8 Adding profile info and exit code behavior. Making version numbers consistent. Upping test number. trinity_ctat parents: 7 diff changeset	1 <tool id="catbash" name="Concatenate datasets" version="1.0.0" profile="17.05">
0 7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	2 <description> concatenate datasets from tail to head</description>
2 2a3972086548 Test concatenate changes trinity_ctat parents: 1 diff changeset	3 <requirements>
4 15f72c57117d Test concatenate changes trinity_ctat parents: 3 diff changeset	4 <requirement type="package" version="2.7">python</requirement>
2 2a3972086548 Test concatenate changes trinity_ctat parents: 1 diff changeset	5 </requirements>
7 43cb585e9e1c Adding some debugging statements. trinity_ctat parents: 6 diff changeset	6
8 323f676857c8 Adding profile info and exit code behavior. Making version numbers consistent. Upping test number. trinity_ctat parents: 7 diff changeset	7 <command detect_errors="exit_code">
1 1e638acde0cf Test concatenate changes trinity_ctat parents: 0 diff changeset	8 <![CDATA[
5 38f80bb7b29c Test concatenate changes trinity_ctat parents: 4 diff changeset	9 python $__tool_directory__/bash_command_executer.py cat
0 7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	10 $input1
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	11 #for $q in $queries
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	12 ${q.input2}
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	13 #end for
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	14 > $out_file1
1 1e638acde0cf Test concatenate changes trinity_ctat parents: 0 diff changeset	15 ]]>
0 7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	16 </command>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	17 <inputs>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	18 <param name="input1" type="data" label="Concatenate Dataset"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	19 <repeat name="queries" title="Dataset">
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	20 <param name="input2" type="data" label="Select" />
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	21 </repeat>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	22 </inputs>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	23 <outputs>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	24 <data name="out_file1" format="input" metadata_source="input1"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	25 </outputs>
7 43cb585e9e1c Adding some debugging statements. trinity_ctat parents: 6 diff changeset	26
0 7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	27 <tests>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	28 <test>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	29 <param name="input1" value="Sp_ds.left.fq"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	30 <param name="input2" value="Sp_hs.left.fq"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	31 <output name="out_file1" file="Sp.cat_ds_hs.left.fq">
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	32 <assert_contents>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	33 <has_line_matching expression=".+" />
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	34 </assert_contents>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	35 </output>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	36 </test>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	37 <test>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	38 <param name="input1" value="Sp_ds.right.fq"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	39 <param name="input2" value="Sp_hs.right.fq"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	40 <output name="out_file1" file="Sp.cat_ds_hs.right.fq">
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	41 <assert_contents>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	42 <has_line_matching expression=".+" />
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	43 </assert_contents>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	44 </output>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	45 </test>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	46 <!--TODO: if possible, enhance the underlying test code to handle this test
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	47 the problem is multiple params with the same name "input2"
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	48 <test>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	49 <param name="input1" value="1.bed"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	50 <param name="input2" value="2.bed"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	51 <param name="input2" value="3.bed"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	52 <output name="out_file1" file="cat_wrapper_out2.bed"/>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	53 </test>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	54 -->
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	55 </tests>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	56 <help>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	57 .. class:: infomark
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	58
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	59 Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly.
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	60
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	61 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	62
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	63 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	64 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	65 </help>
7a974f285033 Initial commit with concatenate and trinity tools. Still testing. trinity_ctat parents: diff changeset	66 </tool>

Mercurial > repos > trinity_ctat > concatenate

annotate concatenate.xml @ 8:323f676857c8 draft default tip