awkscript: awkscript.xml annotate

annotate awkscript.xml @ 4:7966a43dbc9e draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit ada9e882d260555d79c64e38a8ce26b1e84966f0"

author	brinkmanlab
date	Fri, 06 Nov 2020 23:48:35 +0000
parents	ceac6ffb3865
children	df0c8f33c8ea

rev	line source
4 7966a43dbc9e "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit ada9e882d260555d79c64e38a8ce26b1e84966f0" brinkmanlab parents: 3 diff changeset	1 <tool id="awkscript" name="AWK Script" version="1.0" profile="16.04">
0 7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	2 <description>Transform, modify, or generate data</description>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	3 <edam_topics>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	4 <edam_topic>topic_0769</edam_topic>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	5 </edam_topics>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	6 <edam_operations>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	7 <edam_operation>operation_3429</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	8 <edam_operation>operation_3778</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	9 <edam_operation>operation_3434</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	10 <edam_operation>operation_2409</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	11 </edam_operations>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	12 <requirements>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	13 <requirement type="package" version="5.0.1">gawk</requirement>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	14 </requirements>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	15 <version_command>awk --version \| head -n 1</version_command>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	16 <command><![CDATA[
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	17 #set $tool_input = 0
2 c6c81e6e1ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 5c1b5fac50eb1e77d59c2df576e9b54b1b0a1b44" brinkmanlab parents: 1 diff changeset	18 env -i
0 7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	19 #for env in $envs
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	20 '$env.name'='$env.val'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	21 #end for
3 ceac6ffb3865 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 00868930fc05f48a702fe8357b58f004cf899238" brinkmanlab parents: 2 diff changeset	22 \$(which awk)
0 7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	23 --sandbox
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	24 -v FS=' '
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	25 -v OFS=' '
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	26 -f '$awk_script'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	27 #for group in $infiles
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	28 tool_input=$tool_input
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	29 #set $tool_input+=1
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	30 #if $group.input_type_selection.multiple
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	31 #set $inputs = $group.input_type_selection.infile
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	32 ## Allow capturing the collection id in the program
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	33 ## tool_input_id='$inputs.element_identifier' FIXME collections dont expose their label to tools.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	34 #else
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	35 #set $inputs = [$group.input_type_selection.infile]
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	36 #end if
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	37 #for file in $inputs
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	38 tool_input_id='$file.element_identifier'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	39 '$file'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	40 #end for
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	41 #end for
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	42 > '$outfile'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	43 ]]></command>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	44 <configfiles>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	45 <configfile name="awk_script">$code</configfile>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	46 </configfiles>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	47 <inputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	48 <repeat name="infiles" title="Inputs">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	49 <conditional name="input_type_selection">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	50 <param name="multiple" type="boolean" checked="false" label="Accept multiple" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	51 <when value="false">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	52 <param name="infile" format="txt" type="data" label="Single file to process" help="A separate execution will occur for each provided file"/>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	53 </when>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	54 <when value="true">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	55 <param name="infile" format="txt" type="data" multiple="true" label="File or collection to process" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	56 </when>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	57 </conditional>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	58 </repeat>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	59 <param name="code" type="text" area="true" size="5x35" label="AWK Program" help="">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	60 <sanitizer sanitize="false" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	61 </param>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	62 <repeat name="envs" title="Environment Variables">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	63 <param name="name" type="text" label="Name">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	64 <sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	65 <valid initial="string.printable">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	66 <remove value="'" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	67 </valid>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	68 </sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	69 </param>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	70 <param name="val" type="text" label="Value">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	71 <sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	72 <valid initial="string.printable">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	73 <remove value="'" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	74 </valid>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	75 </sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	76 </param>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	77 </repeat>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	78 </inputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	79 <outputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	80 <data name="outfile" format="txt" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	81 </outputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	82 <tests>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	83 <test>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	84 <repeat name="envs">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	85 <param name="name" value="message" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	86 <param name="val" value="Success!" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	87 </repeat>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	88 <param name="code" value="BEGIN { print ENVIRON["message"]; }" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	89 <output name="outfile">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	90 <assert_contents>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	91 <has_text text="Success!" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	92 </assert_contents>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	93 </output>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	94 </test>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	95 </tests>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	96 <help><![CDATA[
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	97 GNU AWK Script
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	98
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	99 Several kinds of tasks occur repeatedly when working with text files.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	100 You might want to extract certain lines and discard the rest. Or you may need to make changes wherever
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	101 certain patterns appear, but leave the rest of the file alone. Such jobs are often easy with awk.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	102 The awk utility interprets a special-purpose programming language that makes it easy to handle simple data-reformatting jobs.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	103
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	104 Each input can be set to single, causing any input collections to map over the tool running, a new instance for each.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	105 Setting the input to multiple will pass the entire collection to a single instance of the tool, allowing aggregation of the input data.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	106 A mixture of single and multiple inputs is allowed, the single inputs being mapped over and the multiple inputs passed to each instance.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	107 This tool is also able to operate with no inputs, generating data for whatever purpose.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	108
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	109 See [GNU AWK Users Guide](https://www.gnu.org/software/gawk/manual/gawk.html) for more information.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	110
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	111 A variable 'tool_input' will be set to the index of the inputs, in order.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	112 You can combine this with ARGIND to determine which file you are currently operating on and its position in any possible input collection.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	113 A variable 'tool_input_id' is also set specifying the current inputs dataset name or collection id.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	114 Beware that ARGIND will increment 3 between inputs as one is consumed setting tool_input and another setting tool_input_id.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	115
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	116 The environment inputs allow you to generalise your scripts, specifying constants with the tool invocation, or allow attaching simple workflow inputs.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	117 Environment variables are accessible via [ENVIRON](https://www.gnu.org/software/gawk/manual/gawk.html#index-environment-variables_002c-in-ENVIRON-array).
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	118
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	119 Due to a limitation in Galaxy, all output is assigned the 'txt' type. This can be changed in the tool settings in a workflow or modifying the dataset after invocation.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	120
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	121 gawk is run with the [sandbox](https://www.gnu.org/software/gawk/manual/gawk.html#index-sandbox-mode) argument, disabling some functionality.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	122 ]]></help>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	123 <citations>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	124 <citation type="doi">10.5281/zenodo.3364789</citation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	125 </citations>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e" brinkmanlab parents: diff changeset	126 </tool>

Mercurial > repos > brinkmanlab > awkscript

annotate awkscript.xml @ 4:7966a43dbc9e draft