Mercurial > repos > rnateam > peakachu
comparison peakachu.xml @ 4:940b1d632f4d draft default tip
"planemo upload for repository https://github.com/tbischler/PEAKachu commit 23fac1009bde8648151e533ce12c9f3d2f787a65-dirty"
| author | rnateam |
|---|---|
| date | Mon, 13 Sep 2021 17:20:47 +0000 |
| parents | 886f5adba83d |
| children |
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| 3:886f5adba83d | 4:940b1d632f4d |
|---|---|
| 1 <tool id="peakachu" name="PEAKachu" version="0.1.0.2"> | 1 <tool id="peakachu" name="PEAKachu" version="0.2.0+galaxy0" profile="20.01"> |
| 2 <description>Calls Peaks in CLIP data</description> | 2 <description>Calls Peaks in CLIP data</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.6">python</requirement> | 4 <requirement type="package" version="3.6">python</requirement> |
| 5 <requirement type="package" version="3.4.1">r-base</requirement> | 5 <requirement type="package" version="4.1.0">r-base</requirement> |
| 6 <requirement type="package" version="0.1.0">peakachu</requirement> | 6 <requirement type="package" version="0.2.0">peakachu</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <version_command> | 8 <version_command> |
| 9 <![CDATA[ | 9 <![CDATA[ |
| 10 peakachu --version | 10 peakachu --version |
| 11 ]]> | 11 ]]> |
| 57 --het_p_val_threshold $mode.het_p_val_threshold | 57 --het_p_val_threshold $mode.het_p_val_threshold |
| 58 --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold | 58 --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold |
| 59 #end if | 59 #end if |
| 60 --norm_method $mode.norm_method.norm_method_selector | 60 --norm_method $mode.norm_method.norm_method_selector |
| 61 #if str($mode.norm_method.norm_method_selector) == 'manual': | 61 #if str($mode.norm_method.norm_method_selector) == 'manual': |
| 62 --size_factors $size_factors | 62 --size_factors '${mode.norm_method.size_factors}' |
| 63 #end if | 63 #end if |
| 64 --mad_multiplier $mad_multiplier | 64 --mad_multiplier $mad_multiplier |
| 65 --fc_cutoff $fc_cutoff | 65 --fc_cutoff $fc_cutoff |
| 66 --padj_threshold $padj_threshold | 66 --padj_threshold $padj_threshold |
| 67 | 67 |
| 111 <when value="adaptive"> | 111 <when value="adaptive"> |
| 112 <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/> | 112 <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/> |
| 113 <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/> | 113 <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/> |
| 114 <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/> | 114 <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/> |
| 115 <conditional name="norm_method"> | 115 <conditional name="norm_method"> |
| 116 <param name="norm_method_selector" type="select" label="Normalisation Method."> | 116 <param name="norm_method_selector" type="select" label="Normalisation Method"> |
| 117 <option value="deseq" selected="True">DESeq2</option> | 117 <option value="deseq" selected="True">DESeq2</option> |
| 118 <option value="manual">Manual</option> | 118 <option value="manual">Manual</option> |
| 119 <option value="none">None</option> | 119 <option value="none">None</option> |
| 120 </param> | 120 </param> |
| 121 <when value="deseq"/> | 121 <when value="deseq"/> |
| 135 <param name="stat_test" type="select" label="Statistical Test"> | 135 <param name="stat_test" type="select" label="Statistical Test"> |
| 136 <option value="gtest" selected="True">gtest</option> | 136 <option value="gtest" selected="True">gtest</option> |
| 137 <option value="deseq">DESeq2</option> | 137 <option value="deseq">DESeq2</option> |
| 138 </param> | 138 </param> |
| 139 <conditional name="norm_method"> | 139 <conditional name="norm_method"> |
| 140 <param name="norm_method_selector" type="select" label="Normalisation Method."> | 140 <param name="norm_method_selector" type="select" label="Normalisation Method"> |
| 141 <option value="tmm" selected="True">TMM</option> | 141 <option value="tmm" selected="True">TMM</option> |
| 142 <option value="deseq">DESeq2</option> | 142 <option value="deseq">DESeq2</option> |
| 143 <option value="count">Count</option> | 143 <option value="count">Count</option> |
| 144 <option value="manual">Manual</option> | 144 <option value="manual">Manual</option> |
| 145 <option value="none">None</option> | 145 <option value="none">None</option> |
| 147 <when value="deseq"/> | 147 <when value="deseq"/> |
| 148 <when value="tmm"/> | 148 <when value="tmm"/> |
| 149 <when value="count"/> | 149 <when value="count"/> |
| 150 <when value="none"/> | 150 <when value="none"/> |
| 151 <when value="manual"> | 151 <when value="manual"> |
| 152 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE"> | 152 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be separated by SPACE"> |
| 153 <sanitizer> | 153 <sanitizer> |
| 154 <valid initial="default"/> | 154 <valid initial="default"/> |
| 155 </sanitizer> | 155 </sanitizer> |
| 156 </param> | 156 </param> |
| 157 </when> | 157 </when> |