comparison filter_low_expr_transcripts.xml @ 9:e659504d166c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4

8:6f0fb35b799c

<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@.0">
    <description>from a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
        filter_low_expr_transcripts.pl
            --matrix '$matrix'
            --transcripts '$assembly'

            #if $additional_params.gene_map.has_gene_map == "no":
                --gene_to_trans_map '$additional_params.gene_map.gene_trans_map'
            #else
                --trinity_mode
            #end if

            #if str($min_expr_any):
                --min_expr_any $min_expr_any
            #end if

9:e659504d166c

<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@">
    <description>from a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[

        #if $additional_params.gene_map.has_gene_map == "yes":
            get_Trinity_gene_to_trans_map.pl '$assembly' > gene_to_trans.map &&
        #else:
            ln -f -s '$additional_params.gene_map.gene_trans_map' gene_to_trans.map &&
        #end if

        filter_low_expr_transcripts.pl
            --matrix '$matrix'
            --transcripts '$assembly'

            --gene_to_trans_map gene_to_trans.map

            #if str($min_expr_any):
                --min_expr_any $min_expr_any
            #end if