comparison peakachu.xml @ 3:886f5adba83d draft

planemo upload for repository https://github.com/tbischler/PEAKachu commit 4a5c3c370df53a00aded3eaae40f3a8e4a263385-dirty

2:49a5a2e86c84

        --padj_threshold $padj_threshold

        &&
        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
        then 
            cat ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
            mv peaks.tsv '$peak_tables' &&
            cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
            mv peak_annotations.gff '$peak_annotations' &&
            mv ./tmp_output/plots/Initial*.png '$MA_plot';
        else 
            echo "No Peaks Found" >&2;
        fi 

3:886f5adba83d

        --padj_threshold $padj_threshold

        &&
        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
        then 
            sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv &&
            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
            mv peaks.tsv '$peak_tables' &&
            awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff &&
            mv peak_annotations.gff '$peak_annotations' &&
            mv ./tmp_output/plots/Initial*.png '$MA_plot';
        else 
            echo "No Peaks Found" >&2;
        fi