Repository 'cuffdiff'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff

Changeset 16:af3e173cad7f (2020-07-03)
Previous changeset 15:43b36b3d4333 (2020-06-16) Next changeset 17:43221aef70e2 (2021-11-27)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
modified:
cuff_macros.xml
cuffdiff_wrapper.xml
b
diff -r 43b36b3d4333 -r af3e173cad7f cuff_macros.xml
--- a/cuff_macros.xml Tue Jun 16 13:00:02 2020 -0400
+++ b/cuff_macros.xml Fri Jul 03 11:43:55 2020 -0400
[
b'@@ -1,91 +1,95 @@\n <macros>\n-  <token name="@VERSION@">2.2.1</token>\n+    <token name="@VERSION@">2.2.1</token>\n+\n+    <xml name="requirements">\n+        <requirements>\n+            <requirement type="package" version="2.2.1">cufflinks</requirement>\n+            <yield />\n+        </requirements>\n+    </xml>\n \n-  <xml name="requirements">\n-    <requirements>\n-      <requirement type="package" version="2.2.1">cufflinks</requirement>\n-      <yield />\n-    </requirements>\n-  </xml>\n+    <xml name="conditions_repeat" token_format="">\n+        <repeat name="conditions" title="Condition" min="2">\n+            <param name="name" label="Condition name" type="text">\n+                <validator type="empty_field" message="You must provide a condition name" />\n+                <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator>\n+            </param>\n+            <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/>\n+        </repeat>\n+    </xml>\n \n-  <xml name="condition_inputs">\n-    <!-- DEFAULT : use BAM/SAM files -->\n-    <conditional name="in_type">\n-        <param name="set_in_type" type="select" label="Input data type"\n-            help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">\n-            <option value="BAM">SAM/BAM</option>\n-            <option value="CXB">Cuffquant (CXB)</option>\n-            <option value="CONDITION_LIST">List of single replicate conditions</option>\n-            <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>\n-        </param>\n-        <when value="BAM">\n-            <repeat name="conditions" title="Condition" min="2">\n-                <param name="name" label="Condition name" type="text"/>\n-                <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>\n-            </repeat>\n-        </when>\n-        <when value="CXB">\n-            <repeat name="conditions" title="Condition" min="2">\n-                <param name="name" label="Condition name" type="text"/>\n-                <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>\n-            </repeat>\n-        </when>\n-        <when value="CONDITION_LIST">\n-            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />\n-        </when>\n-        <when value="CONDITION_REPLICATE_LIST">\n-            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />\n-        </when>\n-    </conditional>\n-  </xml>\n-  <token name="@CONDITION_SAMPLES@">\n-            #if $in_type.set_in_type in [\'BAM\', \'CXB\']\n-                #for $condition in $in_type.conditions:\n-                    #set samples = \',\'.join( [ str( $sample ) for $sample in $condition.samples ] )\n-                    \'$samples\'\n-                #end for\n-            #elif $in_type.set_in_type == \'CONDITION_LIST\'\n-                #for $sample in $in_type.conditions:\n-                    \'$sample\'\n-                #end for\n-            #elif $in_type.set_in_type == \'CONDITION_REPLICATE_LIST\'\n-                #for $condition_list in $in_type.conditions:\n-                    #set samples = \',\'.join( [ str( $sample ) for $sample in $condition_list ] )\n-                    \'$samples\'\n-                #end for\n-            #end if\n-  </token>\n-  <token name="@CONDITION_LABELS@">\n-            #import re\n-            #if $in_type.set_in_type in [\'BAM\', \'CXB\']\n-                #set labels = \'\\\'\' + \'\\\',\\\'\'.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + \'\\\'\'\n-            #elif $in_type.set_in_type in [\'CONDITION_LIST\', \'CONDITION_REPLICATE_LIST\']\n-                #set labels = \'\\\'\' + \'\\\',\\\'\'.join( map(lambda x: re.sub(\'[^\\w\\-_]\', \'_\', x), $in_type.conditions.keys() ) ) + \'\\\'\'\n-            #end if\n-            --labels'..b's\n-  </token>\n-  <xml name="cufflinks_gtf_inputs">\n-    <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />\n-  </xml>\n-  <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[\n-            ## Inputs.\n-            #for $i, $input_file in enumerate($inputs):\n-                ln -s \'${input_file}\' input_$i &&\n-            #end for\n-  ]]></token>\n-  <token name="@CUFFLINKS_GTF_INPUTS@">\n-            ## Inputs.\n-            #for $i, $input_file in enumerate($inputs):\n-                \'input_$i\'\n-            #end for\n-  </token>\n-  <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>\n+    <xml name="condition_inputs">\n+        <!-- DEFAULT : use BAM/SAM files -->\n+        <conditional name="in_type">\n+            <param name="set_in_type" type="select" label="Input data type"\n+                help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">\n+                <option value="BAM">SAM/BAM</option>\n+                <option value="CXB">Cuffquant (CXB)</option>\n+                <option value="CONDITION_LIST">List of single replicate conditions</option>\n+                <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>\n+            </param>\n+            <when value="BAM">\n+                <expand macro="conditions_repeat" format="sam,bam" />\n+            </when>\n+            <when value="CXB">\n+                <expand macro="conditions_repeat" format="cxb" />\n+            </when>\n+            <when value="CONDITION_LIST">\n+                <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />\n+            </when>\n+            <when value="CONDITION_REPLICATE_LIST">\n+                <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />\n+            </when>\n+        </conditional>\n+    </xml>\n+    <token name="@CONDITION_SAMPLES@"><![CDATA[\n+#if $in_type.set_in_type in [\'BAM\', \'CXB\']\n+    #for $condition in $in_type.conditions:\n+        #set samples = \',\'.join([str($sample) for $sample in $condition.samples])\n+        \'$samples\'\n+    #end for\n+#elif $in_type.set_in_type == \'CONDITION_LIST\'\n+    #for $sample in $in_type.conditions:\n+        \'$sample\'\n+    #end for\n+#elif $in_type.set_in_type == \'CONDITION_REPLICATE_LIST\'\n+    #for $condition_list in $in_type.conditions:\n+        #set samples = \',\'.join([str($sample) for $sample in $condition_list])\n+        \'$samples\'\n+    #end for\n+#end if\n+    ]]></token>\n+    <token name="@CONDITION_LABELS@"><![CDATA[\n+#import re\n+#if $in_type.set_in_type in [\'BAM\', \'CXB\']\n+    #set labels = "\',\'".join([str($condition.name) for $condition in $in_type.conditions])\n+#elif $in_type.set_in_type in [\'CONDITION_LIST\', \'CONDITION_REPLICATE_LIST\']\n+    #set labels = "\',\'".join([str($condition).replace(\',\', \'_\') for $condition in $in_type.conditions.keys()])\n+#end if\n+--labels \'$labels\'\n+    ]]></token>\n+    <xml name="cufflinks_gtf_inputs">\n+        <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />\n+    </xml>\n+    <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[\n+## Inputs.\n+#for $i, $input_file in enumerate($inputs):\n+    ln -s \'${input_file}\' input_$i &&\n+#end for\n+    ]]></token>\n+    <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[\n+## Inputs.\n+#for $i, $input_file in enumerate($inputs):\n+    \'input_$i\'\n+#end for\n+    ]]></token>\n+    <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>\n \n-  <xml name="citations">\n-    <citations>\n-        <citation type="doi">10.1038/nbt.1621</citation>\n-        <yield/>\n-    </citations>\n-  </xml>\n+    <xml name="citations">\n+        <citations>\n+            <citation type="doi">10.1038/nbt.1621</citation>\n+            <yield/>\n+        </citations>\n+    </xml>\n \n </macros>\n'
b
diff -r 43b36b3d4333 -r af3e173cad7f cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml Tue Jun 16 13:00:02 2020 -0400
+++ b/cuffdiff_wrapper.xml Fri Jul 03 11:43:55 2020 -0400
b
b'@@ -1,4 +1,4 @@\n-<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.5">\n+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.6">\n     <description>find significant changes in transcript expression, splicing, and promoter use</description>\n     <macros>\n         <import>cuff_macros.xml</import>\n@@ -68,7 +68,7 @@\n             @CONDITION_SAMPLES@\n             #if $generate_sqlite:\n                 &&\n-                Rscript \'$__tool_directory__/cummeRbund.R\' && mv cummeRbund.sqlite \'${output_cummerbund}\'\n+                Rscript \'$__tool_directory__/cummeRbund.R\'\n             #end if\n             ]]>\n     </command>\n@@ -104,21 +104,21 @@\n             </param>\n             <when value="Yes">\n                 <conditional name="seq_source">\n-                  <param name="index_source" type="select" label="Reference sequence data">\n-                    <option value="cached">Locally cached</option>\n-                    <option value="history">History</option>\n-                  </param>\n-                  <when value="cached">\n-                    <param name="index" type="select" label="Using reference genome">\n-                      <options from_data_table="fasta_indexes">\n-                        <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />\n-                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />\n-                      </options>\n+                    <param name="index_source" type="select" label="Reference sequence data">\n+                        <option value="cached">Locally cached</option>\n+                        <option value="history">History</option>\n                     </param>\n-                  </when>\n-                  <when value="history">\n-                      <param name="ref_file" type="data" format="fasta" label="Using reference file" />\n-                  </when>\n+                    <when value="cached">\n+                        <param name="index" type="select" label="Using reference genome">\n+                        <options from_data_table="fasta_indexes">\n+                            <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />\n+                            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />\n+                        </options>\n+                        </param>\n+                    </when>\n+                    <when value="history">\n+                        <param name="ref_file" type="data" format="fasta" label="Using reference file" />\n+                    </when>\n                 </conditional>\n             </when>\n             <when value="No"></when>\n@@ -209,36 +209,36 @@\n         </data>\n         <!-- Standard datasets. -->\n         <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff">\n-                <filter>not omit_tabular_output</filter>\n+            <filter>not omit_tabular_output</filter>\n         </data>\n         <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff">\n-                <filter>not omit_tabular_output</filter>\n+            <filter>not omit_tabular_output</filter>\n         </data>\n         <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff">\n-                <filter>not omit_tabular_output</filter>\n+            <filter>not omit_tabular_output</filter>\n         </data>\n         <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff">\n-                <filter>not omit_tabular_output</filter>\n+            <filter>not omit_tabular_output</fi'..b'name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/>\n-                <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/>\n-                <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/>\n-                <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/>\n-                <output name="genes_exp" file="genes.exp" lines_diff="200"/>\n-                <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/>\n-                <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/>\n-                <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/>\n+            <!--\n+                Use a list collection as conditions input\n+                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam\n+            -->\n+            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />\n+            <param name="generate_sqlite" value="yes" />\n+            <param name="omit_tabular_output" value="yes" />\n+            <conditional name="in_type">\n+                <param name="set_in_type" value="CONDITION_LIST" />\n+                <param name="conditions">\n+                    <collection type="list">\n+                        <element name="q1" value="cuffdiff_in1.sam" />\n+                        <element name="q2" value="cuffdiff_in2.sam" />\n+                    </collection>\n+                </param>\n+            </conditional>\n+            <param name="fdr" value="0.05" />\n+            <param name="min_alignment_count" value="0" />\n+            <param name="do_bias_correction" value="No" />\n+            <param name="do_normalization" value="No" />\n+            <param name="multiread_correct" value="No"/>\n+            <param name="sAdditional" value="No"/>\n+            <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />\n+        </test>\n+        <test>\n+            <!--\n+                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam\n+            -->\n+            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />\n+            <param name="omit_tabular_output" value="no" />\n+            <conditional name="in_type">\n+                <param name="set_in_type" value="BAM" />\n+                <repeat name="conditions">\n+                    <param name="name" value="q1" />\n+                    <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />\n+                </repeat>\n+                <repeat name="conditions">\n+                    <param name="name" value="q2" />\n+                    <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />\n+                </repeat>\n+            </conditional>\n+            <param name="fdr" value="0.05" />\n+            <param name="min_alignment_count" value="0" />\n+            <param name="do_bias_correction" value="No" />\n+            <param name="do_normalization" value="No" />\n+            <param name="multiread_correct" value="No"/>\n+            <param name="sAdditional" value="No"/>\n+            <output name="splicing_diff" file="splicing.diff"/>\n+            <output name="promoters_diff" file="promoters.diff"/>\n+            <output name="cds_diff" file="cds.diff"/>\n+            <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/>\n+            <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/>\n+            <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/>\n+            <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/>\n+            <output name="genes_exp" file="genes.exp" lines_diff="200"/>\n+            <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/>\n+            <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/>\n+            <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/>\n         </test>\n     </tests>\n     <help>\n'