Mercurial > repos > iuc > stacks2_shortreads

comparison stacks_shortreads.xml @ 1:1974fee35ca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:16:13 -0400
parents ad7a60726fc3
children 43e3eeb2e0ec
comparison
equal deleted inserted replaced
0:ad7a60726fc3 1:1974fee35ca7
9 <expand macro="version_cmd"/> 9 <expand macro="version_cmd"/>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @FASTQ_INPUT_FUNCTIONS@ 11 @FASTQ_INPUT_FUNCTIONS@
12 12
13 mkdir stacks_inputs stacks_outputs && 13 mkdir stacks_inputs stacks_outputs &&
14
15 #if $output_log
16 ln -s '$output_log' stacks_outputs/process_shortreads.log &&
17 #end if
14 18
15 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) 19 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
16 $link_command 20 $link_command
17 21
18 22
27 ## advanced options not shared between shortreads and radtags 31 ## advanced options not shared between shortreads and radtags
28 $options_advanced.no_read_trimming 32 $options_advanced.no_read_trimming
29 $options_advanced.mate_pair 33 $options_advanced.mate_pair
30 $options_advanced.no_overhang 34 $options_advanced.no_overhang
31 35
32 #if $output_log
33 && mv stacks_outputs/process_shortreads.log $output_log
34 #end if
35 @PROCESS_FASTQ_POSTPROC@ 36 @PROCESS_FASTQ_POSTPROC@
36 ]]></command> 37 ]]></command>
37 38
38 <inputs> 39 <inputs>
39 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/> 40 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
80 </element> 81 </element>
81 </collection> 82 </collection>
82 </param> 83 </param>
83 <param name="input_type|barcode_encoding" value="--inline_null"/> 84 <param name="input_type|barcode_encoding" value="--inline_null"/>
84 <param name="barcode" value="procrad/barcodes"/> 85 <param name="barcode" value="procrad/barcodes"/>
85 <param name="capture" value="true"/> 86 <param name="capture" value="-D"/>
86 <param name="no_read_trimming" value="--no_read_trimming" /> 87 <param name="no_read_trimming" value="--no_read_trimming" />
87 <param name="mate_pair" value="--mate-pair" /> 88 <param name="mate_pair" value="--mate-pair" />
88 <param name="no_overhang" value="--no_overhang" /> 89 <param name="no_overhang" value="--no_overhang" />
89 <param name="outype" value="gzfastq"/> 90 <param name="outype" value="gzfastq"/>
90 <param name="add_log" value="yes" /> 91 <param name="add_log" value="yes" />
91 <assert_command> 92 <assert_command>
93 <has_text text="-D" />
92 <has_text text="--no_read_trimming" /> 94 <has_text text="--no_read_trimming" />
93 <has_text text="--mate-pair" /> 95 <has_text text="--mate-pair" />
94 <has_text text="--no_overhang" /> 96 <has_text text="--no_overhang" />
95 </assert_command> 97 </assert_command>
96 <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/> 98 <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/>